Starting phenix.real_space_refine on Tue Feb 20 06:19:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9h_22748/02_2024/7k9h_22748.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9h_22748/02_2024/7k9h_22748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9h_22748/02_2024/7k9h_22748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9h_22748/02_2024/7k9h_22748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9h_22748/02_2024/7k9h_22748.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9h_22748/02_2024/7k9h_22748.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 17141 2.51 5 N 4388 2.21 5 O 5381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "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 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 89": "OD1" <-> "OD2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 40": "OE1" <-> "OE2" Residue "L ASP 43": "OD1" <-> "OD2" Residue "L PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 40": "OE1" <-> "OE2" Residue "M PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 83": "OE1" <-> "OE2" Residue "M GLU 85": "OE1" <-> "OE2" Residue "M TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27022 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 6876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 950, 6876 Classifications: {'peptide': 950} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 47, 'TRANS': 902} Chain breaks: 12 Unresolved non-hydrogen bonds: 572 Unresolved non-hydrogen angles: 738 Unresolved non-hydrogen dihedrals: 477 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "B" Number of atoms: 7649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7649 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 49, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 7623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7623 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 80 Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "I" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 812 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 812 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.99, per 1000 atoms: 0.52 Number of scatterers: 27022 At special positions: 0 Unit cell: (132, 147.4, 202.4, 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 112 16.00 O 5381 8.00 N 4388 7.00 C 17141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA r 3 " - " MAN r 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " 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 r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " BETA1-6 " NAG J 1 " - " FUC J 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG b 1 " - " FUC b 2 " " NAG n 1 " - " FUC n 2 " NAG-ASN " NAG A1300 " - " ASN A 61 " " NAG B1300 " - " ASN B 61 " " NAG C1300 " - " ASN C 61 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 603 " " NAG K 1 " - " ASN A 616 " " NAG N 1 " - " ASN A 657 " " NAG O 1 " - " ASN A 709 " " NAG P 1 " - " ASN A 717 " " NAG Q 1 " - " ASN A 801 " " NAG R 1 " - " ASN A1074 " " NAG S 1 " - " ASN A1098 " " NAG T 1 " - " ASN A1134 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 165 " " NAG W 1 " - " ASN B 234 " " NAG X 1 " - " ASN B 282 " " NAG Y 1 " - " ASN B 616 " " NAG Z 1 " - " ASN B 331 " " NAG a 1 " - " ASN B 343 " " NAG b 1 " - " ASN B 603 " " NAG c 1 " - " ASN B 657 " " NAG d 1 " - " ASN B 709 " " NAG e 1 " - " ASN B1098 " " NAG f 1 " - " ASN B 801 " " NAG g 1 " - " ASN B1074 " " NAG h 1 " - " ASN B1134 " " NAG i 1 " - " ASN C 165 " " NAG j 1 " - " ASN C 234 " " NAG k 1 " - " ASN C 282 " " NAG l 1 " - " ASN C 331 " " NAG m 1 " - " ASN C 343 " " NAG n 1 " - " ASN C 603 " " NAG o 1 " - " ASN C 616 " " NAG p 1 " - " ASN C 657 " " NAG q 1 " - " ASN C 709 " " NAG r 1 " - " ASN C 717 " " NAG s 1 " - " ASN C 801 " " NAG t 1 " - " ASN C1074 " " NAG u 1 " - " ASN C1098 " " NAG v 1 " - " ASN C1134 " Time building additional restraints: 12.24 Conformation dependent library (CDL) restraints added in 5.0 seconds 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6314 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 50 sheets defined 24.4% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.803A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.246A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 421 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 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.734A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.670A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.626A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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: 4.027A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.648A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.746A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.051A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.260A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.073A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.895A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.844A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.160A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.747A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.694A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.109A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.137A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.828A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.488A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.278A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.009A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.742A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.723A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.781A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.658A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.990A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.152A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.725A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.209A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.822A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.694A pdb=" N THR H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 removed outlier: 3.771A pdb=" N THR I 90 " --> pdb=" O THR I 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.701A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.457A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.736A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.944A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.922A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.854A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.070A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.070A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.889A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.658A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.571A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.746A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.845A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.459A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.879A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.655A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.842A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AC7, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.779A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.249A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.699A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.632A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.606A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.970A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.574A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.598A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 451 through 454 removed outlier: 4.555A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 495 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.581A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.941A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.941A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.512A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 68 " --> pdb=" O LYS H 81 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.876A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR H 109 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.876A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.744A pdb=" N SER I 7 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.582A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR I 109 " --> pdb=" O ARG I 97 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.524A pdb=" N THR L 5 " --> pdb=" O ARG L 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL L 18 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE L 77 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER L 67 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 9 through 10 removed outlier: 5.962A pdb=" N ALA L 35 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY L 51 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 10 Processing sheet with id=AF3, first strand: chain 'M' and resid 17 through 22 removed outlier: 3.585A pdb=" N ALA M 73 " --> pdb=" O CYS M 22 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER M 65 " --> pdb=" O THR M 76 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 55 through 56 removed outlier: 3.754A pdb=" N LEU M 45 " --> pdb=" O LYS M 41 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY M 51 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA M 35 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL M 99 " --> pdb=" O LEU M 92 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 55 through 56 removed outlier: 3.754A pdb=" N LEU M 45 " --> pdb=" O LYS M 41 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY M 51 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA M 35 " --> pdb=" O GLY M 51 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3036 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: 12.18 Time building geometry restraints manager: 13.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5917 1.33 - 1.45: 6625 1.45 - 1.58: 14899 1.58 - 1.70: 2 1.70 - 1.82: 140 Bond restraints: 27583 Sorted by residual: bond pdb=" C1 NAG m 2 " pdb=" O5 NAG m 2 " ideal model delta sigma weight residual 1.406 1.495 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C1 NAG o 2 " pdb=" O5 NAG o 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG r 2 " pdb=" O5 NAG r 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1 NAG s 2 " pdb=" O5 NAG s 2 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 NAG c 1 " pdb=" O5 NAG c 1 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 27578 not shown) Histogram of bond angle deviations from ideal: 97.65 - 104.95: 490 104.95 - 112.24: 14581 112.24 - 119.53: 8429 119.53 - 126.82: 13821 126.82 - 134.12: 276 Bond angle restraints: 37597 Sorted by residual: angle pdb=" C PRO C 426 " pdb=" CA PRO C 426 " pdb=" CB PRO C 426 " ideal model delta sigma weight residual 110.98 104.20 6.78 1.31e+00 5.83e-01 2.68e+01 angle pdb=" C PRO C 561 " pdb=" N PHE C 562 " pdb=" CA PHE C 562 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" CA PHE C 429 " pdb=" CB PHE C 429 " pdb=" CG PHE C 429 " ideal model delta sigma weight residual 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.54e+01 angle pdb=" CA ASP C 427 " pdb=" C ASP C 427 " pdb=" O ASP C 427 " ideal model delta sigma weight residual 121.19 116.87 4.32 1.10e+00 8.26e-01 1.54e+01 angle pdb=" N TYR B 91 " pdb=" CA TYR B 91 " pdb=" C TYR B 91 " ideal model delta sigma weight residual 109.07 103.89 5.18 1.61e+00 3.86e-01 1.03e+01 ... (remaining 37592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.03: 15973 25.03 - 50.05: 901 50.05 - 75.08: 307 75.08 - 100.11: 268 100.11 - 125.14: 225 Dihedral angle restraints: 17674 sinusoidal: 7864 harmonic: 9810 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -177.82 -89.18 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 178.64 -85.64 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -156.15 70.15 1 1.00e+01 1.00e-02 6.34e+01 ... (remaining 17671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 4621 0.181 - 0.362: 38 0.362 - 0.543: 3 0.543 - 0.724: 2 0.724 - 0.905: 1 Chirality restraints: 4665 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.61e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.66e+00 ... (remaining 4662 not shown) Planarity restraints: 4739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " -0.028 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP B 64 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C1028 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C LYS C1028 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS C1028 " -0.018 2.00e-02 2.50e+03 pdb=" N MET C1029 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 767 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C LEU B 767 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU B 767 " 0.017 2.00e-02 2.50e+03 pdb=" N THR B 768 " 0.016 2.00e-02 2.50e+03 ... (remaining 4736 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 509 2.65 - 3.21: 25431 3.21 - 3.77: 39942 3.77 - 4.34: 53811 4.34 - 4.90: 90929 Nonbonded interactions: 210622 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.085 2.440 nonbonded pdb=" NZ LYS B 378 " pdb=" OH TYR B 380 " model vdw 2.152 2.520 nonbonded pdb=" NZ LYS C 733 " pdb=" OD2 ASP C 775 " model vdw 2.171 2.520 nonbonded pdb=" NE2 GLN I 6 " pdb=" O TYR I 93 " model vdw 2.192 2.520 nonbonded pdb=" OG1 THR M 82 " pdb=" OE1 GLU M 83 " model vdw 2.203 2.440 ... (remaining 210617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 throug \ h 109 or (resid 110 through 112 and (name N or name CA or name C or name O or na \ me CB )) or resid 113 through 128 or (resid 129 and (name N or name CA or name C \ or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 140 or \ resid 165 through 168 or (resid 169 and (name N or name CA or name C or name O \ or name CB )) or resid 170 through 187 or (resid 188 and (name N or name CA or n \ ame C or name O or name CB )) or resid 189 through 190 or (resid 191 and (name N \ or name CA or name C or name O or name CB )) or resid 192 through 195 or (resid \ 196 and (name N or name CA or name C or name O or name CB )) or resid 200 throu \ gh 210 or (resid 211 through 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 241 or (resid 242 through 263 and (name N or name \ CA or name C or name O or name CB )) or resid 265 through 280 or (resid 281 and \ (name N or name CA or name C or name O or name CB )) or resid 282 through 323 o \ r (resid 324 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 25 through 567 or (resid 568 and (name N or name CA or name C or name O or name \ CB )) or resid 569 through 570 or (resid 571 and (name N or name CA or name C or \ name O or name CB )) or resid 572 through 581 or (resid 582 through 583 and (na \ me N or name CA or name C or name O or name CB )) or resid 584 through 585 or (r \ esid 586 and (name N or name CA or name C or name O or name CB )) or resid 587 t \ hrough 613 or (resid 614 and (name N or name CA or name C or name O or name CB ) \ ) or resid 615 through 618 or (resid 619 and (name N or name CA or name C or nam \ e O or name CB )) or resid 620 through 676 or resid 690 through 744 or (resid 74 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 746 through \ 810 or (resid 811 and (name N or name CA or name C or name O or name CB )) or re \ sid 812 through 827 or resid 856 through 866 or (resid 867 through 868 and (name \ N or name CA or name C or name O or name CB )) or resid 869 through 920 or (res \ id 921 and (name N or name CA or name C or name O or name CB )) or resid 922 thr \ ough 939 or (resid 940 and (name N or name CA or name C or name O or name CB )) \ or resid 941 through 984 or (resid 985 and (name N or name CA or name C or name \ O or name CB )) or resid 986 through 987 or (resid 988 through 989 and (name N o \ r name CA or name C or name O or name CB )) or resid 990 through 1117 or (resid \ 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 thro \ ugh 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name O \ or name CB )) or resid 1147 or resid 1300)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 through 112 and (name N or name CA o \ r name C or name O or name CB )) or resid 113 through 131 or (resid 132 and (nam \ e N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 thro \ ugh 138 and (name N or name CA or name C or name O or name CB )) or resid 139 th \ rough 140 or resid 165 through 168 or (resid 169 and (name N or name CA or name \ C or name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or \ name CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 \ and (name N or name CA or name C or name O or name CB )) or resid 192 through 1 \ 96 or resid 200 through 210 or (resid 211 and (name N or name CA or name C or na \ me O or name CB )) or (resid 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 223 or (resid 224 and (name N or \ name CA or name C or name O or name CB )) or resid 225 through 238 or (resid 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 2 \ 63 or resid 265 through 308 or (resid 309 and (name N or name CA or name C or na \ me O or name CB )) or resid 310 through 323 or (resid 324 and (name N or name CA \ or name C or name O or name CB )) or resid 325 through 332 or (resid 333 throug \ h 334 and (name N or name CA or name C or name O or name CB )) or resid 335 thro \ ugh 339 or (resid 340 and (name N or name CA or name C or name O or name CB )) o \ r resid 341 through 344 or (resid 345 through 360 and (name N or name CA or name \ C or name O or name CB )) or resid 361 or (resid 362 through 378 and (name N or \ name CA or name C or name O or name CB )) or resid 379 or (resid 380 and (name \ N or name CA or name C or name O or name CB )) or resid 381 or (resid 382 throug \ h 383 and (name N or name CA or name C or name O or name CB )) or resid 384 or ( \ resid 385 through 390 and (name N or name CA or name C or name O or name CB )) o \ r resid 391 or (resid 392 through 403 and (name N or name CA or name C or name O \ or name CB )) or resid 404 or (resid 405 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 or (resid 427 through 430 and (name N or name CA or name C or name O or \ name CB )) or resid 431 through 432 or (resid 433 through 445 and (name N or nam \ e CA or name C or name O or name CB )) or resid 446 through 447 or (resid 448 th \ rough 454 and (name N or name CA or name C or name O or name CB )) or (resid 462 \ and (name N or name CA or name C or name O or name CB )) or resid 463 or (resid \ 464 through 466 and (name N or name CA or name C or name O or name CB )) or res \ id 491 or (resid 492 through 495 and (name N or name CA or name C or name O or n \ ame CB )) or resid 496 or (resid 497 through 498 and (name N or name CA or name \ C or name O or name CB )) or resid 499 or (resid 500 through 501 and (name N or \ name CA or name C or name O or name CB )) or resid 502 or (resid 503 and (name N \ or name CA or name C or name O or name CB )) or resid 504 or (resid 505 through \ 506 and (name N or name CA or name C or name O or name CB )) or resid 507 or (r \ esid 508 through 515 and (name N or name CA or name C or name O or name CB )) or \ (resid 522 through 524 and (name N or name CA or name C or name O or name CB )) \ or resid 525 through 528 or (resid 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA o \ r name C or name O or name CB )) or resid 555 through 793 or (resid 794 and (nam \ e N or name CA or name C or name O or name CB )) or resid 795 or (resid 796 and \ (name N or name CA or name C or name O or name CB )) or resid 797 through 810 or \ (resid 811 and (name N or name CA or name C or name O or name CB )) or resid 81 \ 2 through 866 or (resid 867 through 868 and (name N or name CA or name C or name \ O or name CB )) or resid 869 through 939 or (resid 940 and (name N or name CA o \ r name C or name O or name CB )) or resid 941 through 984 or (resid 985 and (nam \ e N or name CA or name C or name O or name CB )) or resid 986 through 987 or (re \ sid 988 through 989 and (name N or name CA or name C or name O or name CB )) or \ resid 990 through 1141 or (resid 1142 and (name N or name CA or name C or name O \ or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name \ N or name CA or name C or name O or name CB )) or resid 1147 or resid 1300)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 through 110 or (resid 111 through 112 and (name N or name CA or name C or n \ ame O or name CB )) or resid 113 through 128 or (resid 129 and (name N or name C \ A or name C or name O or name CB )) or resid 130 through 134 or (resid 135 throu \ gh 138 and (name N or name CA or name C or name O or name CB )) or resid 139 thr \ ough 140 or resid 165 through 187 or (resid 188 and (name N or name CA or name C \ or name O or name CB )) or resid 189 through 195 or (resid 196 and (name N or n \ ame CA or name C or name O or name CB )) or resid 200 through 211 or resid 215 t \ hrough 217 or (resid 218 and (name N or name CA or name C or name O or name CB ) \ ) or resid 219 through 223 or (resid 224 and (name N or name CA or name C or nam \ e O or name CB )) or resid 225 through 238 or (resid 239 and (name N or name CA \ or name C or name O or name CB )) or resid 240 through 308 or (resid 309 and (na \ me N or name CA or name C or name O or name CB )) or resid 310 through 332 or (r \ esid 333 through 334 and (name N or name CA or name C or name O or name CB )) or \ resid 335 through 339 or (resid 340 and (name N or name CA or name C or name O \ or name CB )) or resid 341 through 344 or (resid 345 through 360 and (name N or \ name CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 \ and (name N or name CA or name C or name O or name CB )) or resid 379 or (resid \ 380 and (name N or name CA or name C or name O or name CB )) or resid 381 or (r \ esid 382 through 383 and (name N or name CA or name C or name O or name CB )) or \ resid 384 or (resid 385 through 390 and (name N or name CA or name C or name O \ or name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or n \ ame C or name O or name CB )) or resid 404 or (resid 405 through 411 and (name N \ or name CA or name C or name O or name CB )) or resid 412 through 413 or (resid \ 414 through 415 and (name N or name CA or name C or name O or name CB )) or res \ id 416 or (resid 417 through 425 and (name N or name CA or name C or name O or n \ ame CB )) or resid 426 or (resid 427 through 430 and (name N or name CA or name \ C or name O or name CB )) or resid 431 through 432 or (resid 433 through 445 and \ (name N or name CA or name C or name O or name CB )) or resid 446 through 447 o \ r (resid 448 through 454 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 462 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 or (resid 464 through 466 and (name N or name CA or name C or name O or na \ me CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 or (resid 500 through 501 \ and (name N or name CA or name C or name O or name CB )) or resid 502 or (resid \ 503 and (name N or name CA or name C or name O or name CB )) or resid 504 or (re \ sid 505 through 506 and (name N or name CA or name C or name O or name CB )) or \ resid 507 or (resid 508 through 515 and (name N or name CA or name C or name O o \ r name CB )) or (resid 522 through 524 and (name N or name CA or name C or name \ O or name CB )) or resid 525 through 527 or (resid 528 through 529 and (name N o \ r name CA or name C or name O or name CB )) or resid 530 through 553 or (resid 5 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 555 through \ 567 or (resid 568 and (name N or name CA or name C or name O or name CB )) or r \ esid 569 through 570 or (resid 571 and (name N or name CA or name C or name O or \ name CB )) or resid 572 through 581 or (resid 582 through 583 and (name N or na \ me CA or name C or name O or name CB )) or resid 584 through 585 or (resid 586 a \ nd (name N or name CA or name C or name O or name CB )) or resid 587 through 618 \ or (resid 619 and (name N or name CA or name C or name O or name CB )) or resid \ 620 through 645 or (resid 646 through 647 and (name N or name CA or name C or n \ ame O or name CB )) or resid 648 through 793 or (resid 794 and (name N or name C \ A or name C or name O or name CB )) or resid 795 or (resid 796 and (name N or na \ me CA or name C or name O or name CB )) or resid 797 through 920 or (resid 921 a \ nd (name N or name CA or name C or name O or name CB )) or resid 922 through 111 \ 7 or (resid 1118 and (name N or name CA or name C or name O or name CB )) or res \ id 1119 through 1141 or (resid 1142 and (name N or name CA or name C or name O o \ r name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147 or resid 1300)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'u' selection = chain 'v' } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'k' and resid 1) selection = (chain 'l' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'p' and resid 1) selection = (chain 'q' and resid 1) selection = (chain 's' and resid 1) selection = (chain 't' and resid 1) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 7.570 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 73.620 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 27583 Z= 0.444 Angle : 0.831 8.856 37597 Z= 0.419 Chirality : 0.059 0.905 4665 Planarity : 0.005 0.066 4695 Dihedral : 26.135 125.136 11234 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.18 % Allowed : 1.10 % Favored : 98.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3325 helix: 1.29 (0.19), residues: 694 sheet: 0.01 (0.17), residues: 932 loop : -1.42 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 64 HIS 0.007 0.001 HIS C1064 PHE 0.036 0.002 PHE C 559 TYR 0.039 0.002 TYR B 495 ARG 0.026 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 206 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 708 SER cc_start: 0.7827 (t) cc_final: 0.7596 (m) REVERT: B 200 TYR cc_start: 0.7402 (m-80) cc_final: 0.7197 (m-10) REVERT: B 408 ARG cc_start: 0.8769 (tmm160) cc_final: 0.8445 (tmm160) REVERT: B 505 TYR cc_start: 0.8748 (m-10) cc_final: 0.8432 (m-80) REVERT: C 429 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8502 (t80) REVERT: H 36 TRP cc_start: 0.5978 (m100) cc_final: 0.5084 (m100) REVERT: H 63 LEU cc_start: 0.6825 (tp) cc_final: 0.6268 (mm) REVERT: H 73 ASN cc_start: 0.7343 (m110) cc_final: 0.7047 (m-40) REVERT: H 80 LEU cc_start: 0.7599 (tt) cc_final: 0.7274 (mt) REVERT: H 93 TYR cc_start: 0.7433 (m-80) cc_final: 0.6904 (m-10) REVERT: H 95 CYS cc_start: 0.5168 (p) cc_final: 0.4619 (p) REVERT: H 99 ASP cc_start: 0.6948 (t0) cc_final: 0.6609 (p0) REVERT: I 98 LYS cc_start: 0.5836 (mtmt) cc_final: 0.5524 (mtmt) REVERT: I 108 ASP cc_start: 0.4951 (t70) cc_final: 0.4275 (t0) REVERT: L 36 ASN cc_start: 0.6643 (m-40) cc_final: 0.6319 (t0) REVERT: M 49 LEU cc_start: 0.6468 (mt) cc_final: 0.6076 (tt) REVERT: M 50 ILE cc_start: 0.6252 (mm) cc_final: 0.5852 (mm) outliers start: 5 outliers final: 1 residues processed: 209 average time/residue: 0.3553 time to fit residues: 122.5796 Evaluate side-chains 164 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 0.1980 chunk 253 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 135 optimal weight: 20.0000 chunk 262 optimal weight: 3.9990 chunk 101 optimal weight: 0.0570 chunk 159 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 304 optimal weight: 0.8980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1106 GLN C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27583 Z= 0.182 Angle : 0.753 13.204 37597 Z= 0.341 Chirality : 0.054 0.603 4665 Planarity : 0.004 0.047 4695 Dihedral : 23.994 118.862 5752 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.66 % Allowed : 7.74 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3325 helix: 2.16 (0.20), residues: 683 sheet: 0.13 (0.17), residues: 911 loop : -1.17 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 47 HIS 0.003 0.001 HIS C 49 PHE 0.028 0.001 PHE C 559 TYR 0.017 0.001 TYR I 105 ARG 0.006 0.000 ARG I 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 3.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8570 (ptm) cc_final: 0.8367 (ptp) REVERT: B 408 ARG cc_start: 0.8803 (tmm160) cc_final: 0.8494 (tmm160) REVERT: H 36 TRP cc_start: 0.5858 (m100) cc_final: 0.4856 (m100) REVERT: H 77 GLN cc_start: 0.9060 (pt0) cc_final: 0.8548 (pp30) REVERT: H 80 LEU cc_start: 0.7916 (tt) cc_final: 0.7699 (tp) REVERT: H 95 CYS cc_start: 0.4586 (p) cc_final: 0.4068 (p) REVERT: H 99 ASP cc_start: 0.6857 (t0) cc_final: 0.6282 (p0) REVERT: H 107 MET cc_start: 0.6390 (pmm) cc_final: 0.6111 (pmm) REVERT: I 97 ARG cc_start: 0.7041 (ttp-170) cc_final: 0.6311 (ttp-170) REVERT: L 94 TYR cc_start: 0.7954 (m-10) cc_final: 0.7737 (m-10) outliers start: 18 outliers final: 7 residues processed: 196 average time/residue: 0.3896 time to fit residues: 126.4294 Evaluate side-chains 166 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 159 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain L residue 55 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 253 optimal weight: 0.9990 chunk 207 optimal weight: 0.0980 chunk 83 optimal weight: 2.9990 chunk 304 optimal weight: 0.6980 chunk 329 optimal weight: 6.9990 chunk 271 optimal weight: 0.7980 chunk 302 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN B 955 ASN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 ASN ** M 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27583 Z= 0.177 Angle : 0.690 12.391 37597 Z= 0.311 Chirality : 0.050 0.580 4665 Planarity : 0.004 0.046 4695 Dihedral : 19.963 118.757 5749 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.43 % Allowed : 9.79 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3325 helix: 2.44 (0.20), residues: 680 sheet: 0.26 (0.17), residues: 879 loop : -1.10 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 47 HIS 0.004 0.001 HIS L 97 PHE 0.023 0.001 PHE C 559 TYR 0.017 0.001 TYR B 453 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 4.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 990 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: H 36 TRP cc_start: 0.5543 (m100) cc_final: 0.5030 (m100) REVERT: H 77 GLN cc_start: 0.8956 (pt0) cc_final: 0.8515 (pm20) REVERT: H 99 ASP cc_start: 0.6538 (t0) cc_final: 0.6150 (p0) REVERT: I 97 ARG cc_start: 0.7394 (ttp-170) cc_final: 0.6491 (ttp-170) REVERT: L 36 ASN cc_start: 0.7126 (t0) cc_final: 0.6301 (m-40) REVERT: L 38 VAL cc_start: 0.4920 (OUTLIER) cc_final: 0.4337 (t) REVERT: L 50 ILE cc_start: 0.7280 (mp) cc_final: 0.6162 (mt) REVERT: L 89 PHE cc_start: 0.5027 (m-10) cc_final: 0.4811 (m-10) REVERT: M 94 TYR cc_start: 0.7675 (m-80) cc_final: 0.7406 (m-80) REVERT: M 99 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7341 (p) outliers start: 39 outliers final: 13 residues processed: 209 average time/residue: 0.3682 time to fit residues: 127.4562 Evaluate side-chains 177 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 97 HIS Chi-restraints excluded: chain M residue 99 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 6.9990 chunk 229 optimal weight: 20.0000 chunk 158 optimal weight: 0.2980 chunk 33 optimal weight: 50.0000 chunk 145 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 305 optimal weight: 0.0870 chunk 323 optimal weight: 30.0000 chunk 159 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN M 36 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27583 Z= 0.263 Angle : 0.692 13.078 37597 Z= 0.315 Chirality : 0.051 0.583 4665 Planarity : 0.004 0.043 4695 Dihedral : 18.001 117.014 5749 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.69 % Allowed : 11.29 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3325 helix: 2.32 (0.20), residues: 682 sheet: 0.23 (0.17), residues: 918 loop : -1.09 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 47 HIS 0.003 0.001 HIS C 49 PHE 0.033 0.001 PHE C 559 TYR 0.020 0.001 TYR B1067 ARG 0.007 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 162 time to evaluate : 3.103 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7335 (m-80) cc_final: 0.6612 (m-80) REVERT: B 408 ARG cc_start: 0.8579 (tmm160) cc_final: 0.8177 (tmm160) REVERT: B 990 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: C 346 ARG cc_start: 0.7297 (mmm160) cc_final: 0.7023 (mmm160) REVERT: H 16 GLN cc_start: 0.5052 (OUTLIER) cc_final: 0.4813 (pp30) REVERT: H 36 TRP cc_start: 0.5638 (m100) cc_final: 0.4882 (m100) REVERT: H 77 GLN cc_start: 0.8982 (pt0) cc_final: 0.8539 (pm20) REVERT: L 36 ASN cc_start: 0.7161 (t0) cc_final: 0.6483 (m-40) REVERT: L 50 ILE cc_start: 0.7657 (mp) cc_final: 0.6686 (mt) REVERT: M 99 VAL cc_start: 0.8040 (OUTLIER) cc_final: 0.7694 (p) outliers start: 46 outliers final: 22 residues processed: 193 average time/residue: 0.3796 time to fit residues: 120.3331 Evaluate side-chains 179 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain M residue 99 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 133 optimal weight: 0.0980 chunk 276 optimal weight: 0.5980 chunk 223 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B1106 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27583 Z= 0.268 Angle : 0.687 13.121 37597 Z= 0.312 Chirality : 0.050 0.581 4665 Planarity : 0.004 0.047 4695 Dihedral : 16.834 115.036 5749 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.65 % Allowed : 12.32 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3325 helix: 2.28 (0.20), residues: 682 sheet: 0.18 (0.17), residues: 930 loop : -1.07 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 47 HIS 0.003 0.001 HIS C 49 PHE 0.032 0.001 PHE C 559 TYR 0.021 0.001 TYR A 904 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7546 (m-80) cc_final: 0.6766 (m-80) REVERT: B 408 ARG cc_start: 0.8580 (tmm160) cc_final: 0.8183 (tmm160) REVERT: B 752 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9005 (mp) REVERT: B 990 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: C 346 ARG cc_start: 0.7407 (mmm160) cc_final: 0.7092 (mmm160) REVERT: C 505 TYR cc_start: 0.7222 (t80) cc_final: 0.6792 (t80) REVERT: H 16 GLN cc_start: 0.5092 (OUTLIER) cc_final: 0.4506 (pm20) REVERT: H 36 TRP cc_start: 0.5576 (m100) cc_final: 0.4842 (m100) REVERT: H 77 GLN cc_start: 0.9012 (pt0) cc_final: 0.8618 (pm20) REVERT: I 107 MET cc_start: 0.5142 (mmt) cc_final: 0.4471 (tpp) REVERT: L 36 ASN cc_start: 0.7269 (t0) cc_final: 0.6676 (m-40) REVERT: L 50 ILE cc_start: 0.7495 (mp) cc_final: 0.6487 (mt) REVERT: M 99 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7442 (p) outliers start: 45 outliers final: 23 residues processed: 194 average time/residue: 0.3705 time to fit residues: 119.3276 Evaluate side-chains 185 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain M residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 4.9990 chunk 291 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 324 optimal weight: 20.0000 chunk 269 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 26 optimal weight: 50.0000 chunk 107 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN B1106 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27583 Z= 0.271 Angle : 0.689 12.983 37597 Z= 0.312 Chirality : 0.050 0.580 4665 Planarity : 0.004 0.047 4695 Dihedral : 15.740 114.244 5749 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.58 % Allowed : 13.24 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3325 helix: 2.28 (0.20), residues: 682 sheet: 0.16 (0.17), residues: 901 loop : -1.07 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 47 HIS 0.002 0.001 HIS C 49 PHE 0.032 0.001 PHE C 559 TYR 0.020 0.001 TYR L 34 ARG 0.004 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 154 time to evaluate : 2.972 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7644 (m-80) cc_final: 0.6882 (m-80) REVERT: B 408 ARG cc_start: 0.8570 (tmm160) cc_final: 0.8130 (tmm160) REVERT: B 752 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9009 (mp) REVERT: B 990 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: C 298 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7821 (tp30) REVERT: C 346 ARG cc_start: 0.7327 (mmm160) cc_final: 0.7080 (mmm160) REVERT: C 505 TYR cc_start: 0.7428 (t80) cc_final: 0.6974 (t80) REVERT: H 16 GLN cc_start: 0.5251 (OUTLIER) cc_final: 0.4644 (pm20) REVERT: H 36 TRP cc_start: 0.5562 (m100) cc_final: 0.4908 (m100) REVERT: H 77 GLN cc_start: 0.9014 (pt0) cc_final: 0.8590 (pm20) REVERT: I 107 MET cc_start: 0.5162 (mmt) cc_final: 0.4564 (tpp) REVERT: M 92 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7431 (mm) outliers start: 43 outliers final: 24 residues processed: 189 average time/residue: 0.3800 time to fit residues: 117.6703 Evaluate side-chains 181 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain M residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 184 optimal weight: 0.0670 chunk 236 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 272 optimal weight: 0.3980 chunk 180 optimal weight: 2.9990 chunk 322 optimal weight: 50.0000 chunk 202 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1106 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27583 Z= 0.182 Angle : 0.663 12.458 37597 Z= 0.297 Chirality : 0.049 0.569 4665 Planarity : 0.004 0.047 4695 Dihedral : 14.305 115.514 5749 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.43 % Allowed : 13.93 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3325 helix: 2.51 (0.20), residues: 679 sheet: 0.30 (0.17), residues: 845 loop : -1.01 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 47 HIS 0.002 0.000 HIS A1088 PHE 0.022 0.001 PHE C 559 TYR 0.020 0.001 TYR A 904 ARG 0.011 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 161 time to evaluate : 3.577 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7644 (m-80) cc_final: 0.6771 (m-80) REVERT: B 347 PHE cc_start: 0.6739 (m-10) cc_final: 0.6421 (m-80) REVERT: B 408 ARG cc_start: 0.8561 (tmm160) cc_final: 0.8129 (tmm160) REVERT: B 990 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: C 298 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7769 (tp30) REVERT: C 505 TYR cc_start: 0.7612 (t80) cc_final: 0.7043 (t80) REVERT: H 16 GLN cc_start: 0.5314 (OUTLIER) cc_final: 0.4683 (pm20) REVERT: H 36 TRP cc_start: 0.5504 (m100) cc_final: 0.4890 (m100) REVERT: M 92 LEU cc_start: 0.7610 (mm) cc_final: 0.7289 (mm) outliers start: 39 outliers final: 22 residues processed: 192 average time/residue: 0.3733 time to fit residues: 118.2032 Evaluate side-chains 173 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain L residue 55 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 199 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 0.0020 chunk 205 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 30 optimal weight: 0.0470 chunk 253 optimal weight: 1.9990 overall best weight: 0.7690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 ASN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27583 Z= 0.159 Angle : 0.645 12.538 37597 Z= 0.289 Chirality : 0.048 0.559 4665 Planarity : 0.004 0.048 4695 Dihedral : 12.716 118.584 5749 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.47 % Allowed : 14.19 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3325 helix: 2.71 (0.20), residues: 667 sheet: 0.35 (0.17), residues: 855 loop : -0.96 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 47 HIS 0.007 0.001 HIS M 44 PHE 0.020 0.001 PHE A 592 TYR 0.018 0.001 TYR I 109 ARG 0.012 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 163 time to evaluate : 3.144 Fit side-chains REVERT: A 133 PHE cc_start: 0.7536 (m-80) cc_final: 0.6631 (m-80) REVERT: B 347 PHE cc_start: 0.6812 (m-10) cc_final: 0.6444 (m-80) REVERT: B 408 ARG cc_start: 0.8583 (tmm160) cc_final: 0.8159 (tmm160) REVERT: B 752 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9000 (mp) REVERT: B 990 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: C 298 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7765 (tp30) REVERT: C 505 TYR cc_start: 0.7671 (t80) cc_final: 0.7041 (t80) REVERT: H 16 GLN cc_start: 0.5402 (OUTLIER) cc_final: 0.4755 (pm20) REVERT: H 77 GLN cc_start: 0.9003 (pt0) cc_final: 0.8682 (pm20) REVERT: I 51 ILE cc_start: 0.3829 (OUTLIER) cc_final: 0.3603 (tt) REVERT: I 107 MET cc_start: 0.4672 (OUTLIER) cc_final: 0.3263 (tpt) REVERT: M 92 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.6821 (mm) outliers start: 40 outliers final: 26 residues processed: 193 average time/residue: 0.3565 time to fit residues: 115.3863 Evaluate side-chains 187 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain M residue 92 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 293 optimal weight: 3.9990 chunk 309 optimal weight: 50.0000 chunk 282 optimal weight: 4.9990 chunk 300 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 271 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 chunk 299 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1106 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27583 Z= 0.340 Angle : 0.694 13.105 37597 Z= 0.318 Chirality : 0.050 0.578 4665 Planarity : 0.004 0.048 4695 Dihedral : 11.944 120.142 5749 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.39 % Allowed : 14.78 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3325 helix: 2.38 (0.20), residues: 676 sheet: 0.22 (0.17), residues: 869 loop : -1.02 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 47 HIS 0.004 0.001 HIS A1048 PHE 0.036 0.002 PHE C 559 TYR 0.021 0.002 TYR B1067 ARG 0.013 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 155 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7564 (m-80) cc_final: 0.6636 (m-80) REVERT: B 408 ARG cc_start: 0.8604 (tmm160) cc_final: 0.8244 (tmm160) REVERT: B 740 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7803 (tmm) REVERT: B 752 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9004 (mp) REVERT: B 990 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: C 298 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7878 (tp30) REVERT: C 505 TYR cc_start: 0.7731 (t80) cc_final: 0.6902 (t80) REVERT: H 16 GLN cc_start: 0.5355 (OUTLIER) cc_final: 0.4722 (pm20) REVERT: I 51 ILE cc_start: 0.3906 (OUTLIER) cc_final: 0.3674 (tt) REVERT: I 107 MET cc_start: 0.4886 (mmt) cc_final: 0.3425 (tpp) REVERT: M 92 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7022 (mm) outliers start: 38 outliers final: 26 residues processed: 182 average time/residue: 0.3757 time to fit residues: 113.3047 Evaluate side-chains 185 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain M residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 0.7980 chunk 318 optimal weight: 40.0000 chunk 194 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 333 optimal weight: 30.0000 chunk 307 optimal weight: 20.0000 chunk 265 optimal weight: 0.5980 chunk 27 optimal weight: 50.0000 chunk 205 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1106 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27583 Z= 0.293 Angle : 0.669 13.424 37597 Z= 0.308 Chirality : 0.049 0.575 4665 Planarity : 0.004 0.048 4695 Dihedral : 10.987 119.960 5749 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.10 % Allowed : 15.29 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3325 helix: 2.35 (0.20), residues: 676 sheet: 0.15 (0.17), residues: 857 loop : -1.01 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 47 HIS 0.004 0.001 HIS B1064 PHE 0.031 0.001 PHE C 559 TYR 0.021 0.001 TYR I 109 ARG 0.013 0.001 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7560 (m-80) cc_final: 0.6609 (m-80) REVERT: B 408 ARG cc_start: 0.8611 (tmm160) cc_final: 0.8189 (tmm160) REVERT: B 495 TYR cc_start: 0.6263 (OUTLIER) cc_final: 0.5752 (t80) REVERT: B 740 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7810 (tmm) REVERT: B 752 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9007 (mp) REVERT: B 990 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: C 298 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7845 (tp30) REVERT: C 505 TYR cc_start: 0.7772 (t80) cc_final: 0.6885 (t80) REVERT: H 16 GLN cc_start: 0.5300 (OUTLIER) cc_final: 0.4676 (pm20) REVERT: H 77 GLN cc_start: 0.9014 (pt0) cc_final: 0.8597 (pm20) REVERT: I 98 LYS cc_start: 0.6770 (mtmt) cc_final: 0.6568 (mtmt) REVERT: I 107 MET cc_start: 0.4773 (OUTLIER) cc_final: 0.3331 (tpt) REVERT: M 92 LEU cc_start: 0.7616 (mm) cc_final: 0.7094 (mm) outliers start: 30 outliers final: 22 residues processed: 180 average time/residue: 0.3945 time to fit residues: 117.5475 Evaluate side-chains 182 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 211 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 245 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 266 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 33 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1106 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.161825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.105627 restraints weight = 46781.048| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.80 r_work: 0.3314 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27583 Z= 0.151 Angle : 0.618 13.256 37597 Z= 0.282 Chirality : 0.047 0.559 4665 Planarity : 0.004 0.048 4695 Dihedral : 10.067 118.798 5749 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.25 % Allowed : 15.07 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3325 helix: 2.72 (0.20), residues: 667 sheet: 0.25 (0.17), residues: 839 loop : -0.89 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 47 HIS 0.002 0.000 HIS C1048 PHE 0.043 0.001 PHE C 562 TYR 0.019 0.001 TYR A 170 ARG 0.012 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4870.50 seconds wall clock time: 90 minutes 19.29 seconds (5419.29 seconds total)