Starting phenix.real_space_refine on Wed Feb 21 19:23:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uap_26429/02_2024/7uap_26429.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uap_26429/02_2024/7uap_26429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uap_26429/02_2024/7uap_26429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uap_26429/02_2024/7uap_26429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uap_26429/02_2024/7uap_26429.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uap_26429/02_2024/7uap_26429.pdb" } resolution = 2.8 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= 0.106 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 138 5.16 5 C 20083 2.51 5 N 5243 2.21 5 O 6193 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 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "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 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 56": "OD1" <-> "OD2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 72": "OD1" <-> "OD2" Residue "O TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 111": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31657 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8447 Classifications: {'peptide': 1081} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 58, 'TRANS': 1022} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 8447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8447 Classifications: {'peptide': 1081} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 58, 'TRANS': 1022} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 8447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8447 Classifications: {'peptide': 1081} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 58, 'TRANS': 1022} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 833 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "N" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 833 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "P" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 833 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "L" 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: "N" 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: "P" 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: 16.01, per 1000 atoms: 0.51 Number of scatterers: 31657 At special positions: 0 Unit cell: (182.31, 168.92, 168.92, 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 138 16.00 O 6193 8.00 N 5243 7.00 C 20083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 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=2.09 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.01 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 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=2.07 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=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS 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 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1134 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 149 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN B 122 " " NAG J 1 " - " ASN B 149 " " NAG K 1 " - " ASN B 234 " " NAG L 301 " - " ASN L 20 " " NAG N 301 " - " ASN N 20 " " NAG P 301 " - " ASN P 20 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN C 122 " " NAG S 1 " - " ASN C 149 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 12.12 Conformation dependent library (CDL) restraints added in 5.7 seconds 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7350 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 73 sheets defined 21.0% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.191A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.535A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.402A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.524A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 626 through 629 Processing helix chain 'A' and resid 630 through 638 removed outlier: 4.165A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 748 through 754 Processing helix chain 'A' and resid 756 through 783 removed outlier: 4.168A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.251A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.942A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.807A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.248A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.948A 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 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.235A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.534A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.737A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.532A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 626 through 629 Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.899A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 748 through 783 removed outlier: 6.221A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.404A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.970A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.757A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.318A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.241A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.737A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.752A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.830A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 626 through 629 Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.621A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 748 through 783 removed outlier: 4.111A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.517A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.562A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.500A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 967 removed outlier: 4.148A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.701A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1029 removed outlier: 5.222A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.859A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.652A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 29 removed outlier: 3.714A pdb=" N ASN L 29 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.613A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.788A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 29 removed outlier: 3.755A pdb=" N ASN N 29 " --> pdb=" O SER N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.579A pdb=" N ASP N 82 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.938A pdb=" N ILE O 31 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.648A pdb=" N THR O 87 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 29 removed outlier: 3.503A pdb=" N HIS P 28 " --> pdb=" O SER P 26 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN P 29 " --> pdb=" O SER P 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 26 through 29' Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.196A pdb=" N ASP P 82 " --> pdb=" O GLN P 79 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU P 83 " --> pdb=" O SER P 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.307A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.281A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.343A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 145 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.549A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.496A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.413A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.822A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.522A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 586 " --> pdb=" O THR A 553 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 3.520A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 653 through 659 removed outlier: 6.052A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.593A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.593A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.656A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.866A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.540A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.730A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.451A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.555A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.515A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.685A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.578A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.151A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 727 removed outlier: 6.371A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 712 through 727 removed outlier: 6.371A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.718A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.674A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.560A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.554A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AE7, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.530A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.051A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.577A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 327 through 328 removed outlier: 7.984A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 537 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 552 " --> pdb=" O LYS C 537 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.637A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 361 through 362 removed outlier: 5.991A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.764A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AF7, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.959A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.503A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.503A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AG2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.463A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.768A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 56 through 57 removed outlier: 7.064A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA H 93 " --> pdb=" O ASN H 35 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE H 112 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 88 through 89 removed outlier: 3.514A pdb=" N ALA H 88 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AG7, first strand: chain 'L' and resid 44 through 50 removed outlier: 6.803A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.871A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER M 25 " --> pdb=" O GLN M 3 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL M 5 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER M 7 " --> pdb=" O ALA M 21 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU M 20 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 16 through 17 removed outlier: 5.000A pdb=" N GLY M 16 " --> pdb=" O SER M 82B" (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 46 through 51 removed outlier: 5.682A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN M 35 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA M 93 " --> pdb=" O ASN M 35 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE M 112 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AH3, first strand: chain 'N' and resid 44 through 46 Processing sheet with id=AH4, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.701A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER O 25 " --> pdb=" O GLN O 3 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU O 20 " --> pdb=" O LEU O 80 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 34 through 35 removed outlier: 3.578A pdb=" N ILE O 51 " --> pdb=" O MET O 34 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 88 through 89 Processing sheet with id=AH7, first strand: chain 'O' and resid 93 through 95 removed outlier: 4.451A pdb=" N ILE O 112 " --> pdb=" O ARG O 94 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AH9, first strand: chain 'P' and resid 33 through 38 removed outlier: 6.440A pdb=" N ILE P 33 " --> pdb=" O SER P 49 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER P 49 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU P 47 " --> pdb=" O TRP P 35 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'P' and resid 62 through 64 1003 hydrogen bonds defined for protein. 2718 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: 13.48 Time building geometry restraints manager: 13.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.24: 4367 1.24 - 1.42: 9374 1.42 - 1.60: 18473 1.60 - 1.78: 21 1.78 - 1.96: 160 Bond restraints: 32395 Sorted by residual: bond pdb=" C PRO B 897 " pdb=" O PRO B 897 " ideal model delta sigma weight residual 1.233 1.061 0.172 1.24e-02 6.50e+03 1.92e+02 bond pdb=" C PRO A 897 " pdb=" O PRO A 897 " ideal model delta sigma weight residual 1.233 1.085 0.148 1.23e-02 6.61e+03 1.44e+02 bond pdb=" C MET A 902 " pdb=" O MET A 902 " ideal model delta sigma weight residual 1.237 1.116 0.121 1.19e-02 7.06e+03 1.03e+02 bond pdb=" C PRO C 899 " pdb=" O PRO C 899 " ideal model delta sigma weight residual 1.237 1.104 0.133 1.32e-02 5.74e+03 1.02e+02 bond pdb=" C PRO C 897 " pdb=" O PRO C 897 " ideal model delta sigma weight residual 1.233 1.110 0.122 1.24e-02 6.50e+03 9.75e+01 ... (remaining 32390 not shown) Histogram of bond angle deviations from ideal: 72.58 - 88.29: 2 88.29 - 104.00: 502 104.00 - 119.71: 27443 119.71 - 135.41: 16142 135.41 - 151.12: 4 Bond angle restraints: 44093 Sorted by residual: angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 151.12 -36.72 2.30e+00 1.89e-01 2.55e+02 angle pdb=" N PRO A 897 " pdb=" CA PRO A 897 " pdb=" CB PRO A 897 " ideal model delta sigma weight residual 103.32 90.00 13.32 8.40e-01 1.42e+00 2.51e+02 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 149.56 -35.16 2.30e+00 1.89e-01 2.34e+02 angle pdb=" C THR C 941 " pdb=" N PRO C 942 " pdb=" CD PRO C 942 " ideal model delta sigma weight residual 125.00 72.58 52.42 4.10e+00 5.95e-02 1.63e+02 angle pdb=" C THR B 941 " pdb=" N PRO B 942 " pdb=" CD PRO B 942 " ideal model delta sigma weight residual 125.00 75.15 49.85 4.10e+00 5.95e-02 1.48e+02 ... (remaining 44088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.94: 18890 24.94 - 49.88: 887 49.88 - 74.82: 149 74.82 - 99.76: 41 99.76 - 124.70: 10 Dihedral angle restraints: 19977 sinusoidal: 8502 harmonic: 11475 Sorted by residual: dihedral pdb=" CA ASN P 20 " pdb=" C ASN P 20 " pdb=" N LEU P 21 " pdb=" CA LEU P 21 " ideal model delta harmonic sigma weight residual -180.00 -124.13 -55.87 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA VAL P 19 " pdb=" C VAL P 19 " pdb=" N ASN P 20 " pdb=" CA ASN P 20 " ideal model delta harmonic sigma weight residual 180.00 125.38 54.62 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -8.53 -77.47 1 1.00e+01 1.00e-02 7.52e+01 ... (remaining 19974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 5084 0.315 - 0.630: 19 0.630 - 0.945: 5 0.945 - 1.260: 1 1.260 - 1.576: 1 Chirality restraints: 5110 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -0.82 -1.58 2.00e-01 2.50e+01 6.21e+01 chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-01 2.50e+01 2.57e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 5107 not shown) Planarity restraints: 5683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 941 " 0.171 5.00e-02 4.00e+02 2.48e-01 9.84e+01 pdb=" N PRO B 942 " -0.423 5.00e-02 4.00e+02 pdb=" CA PRO B 942 " 0.183 5.00e-02 4.00e+02 pdb=" CD PRO B 942 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 941 " 0.168 5.00e-02 4.00e+02 2.43e-01 9.45e+01 pdb=" N PRO C 942 " -0.413 5.00e-02 4.00e+02 pdb=" CA PRO C 942 " 0.182 5.00e-02 4.00e+02 pdb=" CD PRO C 942 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 891 " 0.121 5.00e-02 4.00e+02 1.85e-01 5.46e+01 pdb=" N PRO A 892 " -0.319 5.00e-02 4.00e+02 pdb=" CA PRO A 892 " 0.114 5.00e-02 4.00e+02 pdb=" CD PRO A 892 " 0.084 5.00e-02 4.00e+02 ... (remaining 5680 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 477 2.61 - 3.18: 27924 3.18 - 3.76: 48118 3.76 - 4.33: 68124 4.33 - 4.90: 109729 Nonbonded interactions: 254372 Sorted by model distance: nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.041 2.520 nonbonded pdb=" OG1 THR C 393 " pdb=" O PRO C 521 " model vdw 2.072 2.440 nonbonded pdb=" OG SER A 383 " pdb=" OE2 GLU C 988 " model vdw 2.105 2.440 nonbonded pdb=" O LYS C 97 " pdb=" OH TYR O 105 " model vdw 2.105 2.440 nonbonded pdb=" O SER B 967 " pdb=" OG SER B 975 " model vdw 2.112 2.440 ... (remaining 254367 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1145 or resid 1301 through 1310)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 1145 or resid 1301 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.500 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 81.110 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 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 0.172 32395 Z= 0.465 Angle : 1.267 52.416 44093 Z= 0.688 Chirality : 0.075 1.576 5110 Planarity : 0.009 0.248 5636 Dihedral : 14.621 124.697 12483 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.08 % Favored : 92.36 % Rotamer: Outliers : 0.29 % Allowed : 1.20 % Favored : 98.51 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.12), residues: 3915 helix: -0.94 (0.18), residues: 723 sheet: -0.68 (0.19), residues: 738 loop : -2.07 (0.11), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.003 TRP C 64 HIS 0.012 0.002 HIS A 655 PHE 0.035 0.003 PHE C 194 TYR 0.055 0.003 TYR A 873 ARG 0.014 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 471 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 MET cc_start: 0.2574 (tpp) cc_final: 0.2347 (mmm) outliers start: 10 outliers final: 5 residues processed: 477 average time/residue: 1.1345 time to fit residues: 663.3672 Evaluate side-chains 297 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 292 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 897 PRO Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 0.0980 chunk 297 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 200 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 308 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 187 optimal weight: 0.7980 chunk 229 optimal weight: 0.6980 chunk 356 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 655 HIS A1010 GLN B 784 GLN B 804 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN B1101 HIS C 69 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 856 ASN C 907 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 HIS L 28 HIS L 54BHIS M 96 GLN ** P 54BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 32395 Z= 0.237 Angle : 0.780 16.007 44093 Z= 0.391 Chirality : 0.054 0.707 5110 Planarity : 0.006 0.175 5636 Dihedral : 10.978 108.492 5525 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.39 % Favored : 93.33 % Rotamer: Outliers : 2.25 % Allowed : 10.30 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3915 helix: 0.13 (0.19), residues: 701 sheet: -0.49 (0.18), residues: 792 loop : -1.91 (0.11), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 64 HIS 0.007 0.002 HIS O 106 PHE 0.030 0.002 PHE C 168 TYR 0.023 0.002 TYR A1067 ARG 0.009 0.001 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 334 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8141 (p) REVERT: A 725 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: A 1139 ASP cc_start: 0.6332 (t0) cc_final: 0.6097 (t0) REVERT: B 493 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6554 (mm-40) REVERT: P 48 MET cc_start: 0.1822 (mpt) cc_final: 0.0690 (tpp) outliers start: 77 outliers final: 24 residues processed: 379 average time/residue: 1.0436 time to fit residues: 499.4796 Evaluate side-chains 297 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 270 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 34 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 357 optimal weight: 10.0000 chunk 386 optimal weight: 5.9990 chunk 318 optimal weight: 1.9990 chunk 354 optimal weight: 30.0000 chunk 121 optimal weight: 4.9990 chunk 286 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A1010 GLN B 148 ASN B 544 ASN B 901 GLN B 965 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN C 271 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 965 GLN H 35 ASN M 96 GLN O 81 GLN ** O 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 32395 Z= 0.376 Angle : 0.805 13.437 44093 Z= 0.401 Chirality : 0.056 0.684 5110 Planarity : 0.006 0.150 5636 Dihedral : 9.588 95.229 5514 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.77 % Favored : 92.92 % Rotamer: Outliers : 4.07 % Allowed : 13.08 % Favored : 82.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3915 helix: 0.36 (0.20), residues: 696 sheet: -0.59 (0.18), residues: 802 loop : -1.84 (0.11), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 64 HIS 0.029 0.002 HIS B1101 PHE 0.033 0.002 PHE C1062 TYR 0.031 0.002 TYR B 917 ARG 0.009 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 308 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7626 (tt) REVERT: A 725 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: B 458 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7507 (mttp) REVERT: B 493 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.6547 (mm-40) REVERT: C 18 LEU cc_start: 0.2806 (OUTLIER) cc_final: 0.2296 (pp) REVERT: C 351 TYR cc_start: 0.6114 (p90) cc_final: 0.5744 (p90) REVERT: H 38 ARG cc_start: 0.4651 (OUTLIER) cc_final: 0.3433 (ttp80) REVERT: H 46 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5644 (pt0) REVERT: O 30 SER cc_start: 0.3846 (OUTLIER) cc_final: 0.3125 (t) outliers start: 139 outliers final: 59 residues processed: 403 average time/residue: 1.0035 time to fit residues: 508.4008 Evaluate side-chains 315 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 248 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain P residue 62 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 30.0000 chunk 268 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 358 optimal weight: 20.0000 chunk 379 optimal weight: 6.9990 chunk 187 optimal weight: 0.0060 chunk 340 optimal weight: 20.0000 chunk 102 optimal weight: 0.3980 overall best weight: 1.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A1010 GLN B 30 ASN B 703 ASN B 965 GLN B1002 GLN C 121 ASN C 164 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 856 ASN C1036 GLN H 35 ASN L 89 GLN M 96 GLN O 81 GLN ** O 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 32395 Z= 0.353 Angle : 0.774 12.647 44093 Z= 0.385 Chirality : 0.054 0.659 5110 Planarity : 0.005 0.067 5636 Dihedral : 9.035 89.643 5514 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.97 % Favored : 92.72 % Rotamer: Outliers : 4.68 % Allowed : 15.10 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3915 helix: 0.37 (0.20), residues: 706 sheet: -0.62 (0.18), residues: 796 loop : -1.77 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 64 HIS 0.007 0.002 HIS H 98 PHE 0.025 0.002 PHE M 78 TYR 0.024 0.002 TYR A1067 ARG 0.009 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 275 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.5716 (t80) REVERT: A 725 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: A 819 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: B 493 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.6410 (mm-40) REVERT: B 1072 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: C 18 LEU cc_start: 0.2797 (OUTLIER) cc_final: 0.2255 (pp) REVERT: C 314 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6459 (mm110) REVERT: C 351 TYR cc_start: 0.6224 (p90) cc_final: 0.5954 (p90) REVERT: C 1031 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: O 30 SER cc_start: 0.3913 (OUTLIER) cc_final: 0.3184 (t) outliers start: 160 outliers final: 73 residues processed: 394 average time/residue: 0.9415 time to fit residues: 473.9978 Evaluate side-chains 328 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 246 time to evaluate : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain L residue 28 HIS Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain P residue 62 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 316 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 5 optimal weight: 0.0980 chunk 282 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 0.8980 chunk 340 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 655 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN C 580 GLN C 710 ASN C 856 ASN H 35 ASN L 89 GLN M 96 GLN ** O 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 32395 Z= 0.270 Angle : 0.727 14.883 44093 Z= 0.359 Chirality : 0.052 0.640 5110 Planarity : 0.005 0.062 5636 Dihedral : 8.619 83.267 5514 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.46 % Favored : 93.26 % Rotamer: Outliers : 4.30 % Allowed : 16.68 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 3915 helix: 0.60 (0.20), residues: 693 sheet: -0.54 (0.18), residues: 798 loop : -1.71 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 64 HIS 0.005 0.001 HIS A1048 PHE 0.017 0.002 PHE A 133 TYR 0.022 0.002 TYR A1067 ARG 0.006 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 274 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.5698 (t80) REVERT: A 725 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7078 (tt0) REVERT: A 819 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: B 458 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7587 (mttp) REVERT: B 493 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6404 (mm-40) REVERT: B 606 ASN cc_start: 0.6654 (t0) cc_final: 0.6353 (m-40) REVERT: B 902 MET cc_start: 0.7977 (tpp) cc_final: 0.7698 (mmm) REVERT: C 54 LEU cc_start: 0.7273 (mm) cc_final: 0.7038 (mm) REVERT: C 351 TYR cc_start: 0.6312 (p90) cc_final: 0.6082 (p90) REVERT: C 455 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7414 (mp) REVERT: C 646 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7248 (mmt180) REVERT: C 725 GLU cc_start: 0.7526 (tt0) cc_final: 0.6952 (tt0) REVERT: C 923 ILE cc_start: 0.8400 (mm) cc_final: 0.8016 (mm) REVERT: C 947 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7875 (tttp) REVERT: C 1031 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7424 (pt0) REVERT: H 38 ARG cc_start: 0.4432 (OUTLIER) cc_final: 0.3249 (ttp80) REVERT: L 48 MET cc_start: 0.4963 (OUTLIER) cc_final: 0.4249 (tpp) REVERT: O 30 SER cc_start: 0.3865 (OUTLIER) cc_final: 0.3219 (t) outliers start: 147 outliers final: 70 residues processed: 384 average time/residue: 1.0376 time to fit residues: 506.7000 Evaluate side-chains 327 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 245 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 127 optimal weight: 6.9990 chunk 342 optimal weight: 30.0000 chunk 75 optimal weight: 0.0470 chunk 223 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 380 optimal weight: 7.9990 chunk 315 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 655 HIS B 703 ASN B1002 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1005 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN ** P 54BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 32395 Z= 0.285 Angle : 0.728 13.696 44093 Z= 0.360 Chirality : 0.052 0.623 5110 Planarity : 0.005 0.064 5636 Dihedral : 8.470 76.159 5514 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.82 % Favored : 92.92 % Rotamer: Outliers : 4.24 % Allowed : 18.00 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 3915 helix: 0.67 (0.20), residues: 687 sheet: -0.50 (0.18), residues: 782 loop : -1.68 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 64 HIS 0.006 0.001 HIS A1048 PHE 0.019 0.002 PHE M 78 TYR 0.021 0.002 TYR A1067 ARG 0.006 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 273 time to evaluate : 3.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6469 (pt) REVERT: A 347 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.5730 (t80) REVERT: A 725 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: A 819 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: A 1113 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: B 493 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6388 (mm-40) REVERT: B 606 ASN cc_start: 0.6683 (m-40) cc_final: 0.6416 (m-40) REVERT: B 902 MET cc_start: 0.8006 (tpp) cc_final: 0.7737 (mmm) REVERT: C 18 LEU cc_start: 0.2891 (OUTLIER) cc_final: 0.2481 (pp) REVERT: C 54 LEU cc_start: 0.7264 (mm) cc_final: 0.7019 (mm) REVERT: C 455 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7408 (mp) REVERT: C 577 ARG cc_start: 0.4895 (OUTLIER) cc_final: 0.3916 (tpp-160) REVERT: C 697 MET cc_start: 0.6353 (ttm) cc_final: 0.6117 (mtt) REVERT: C 923 ILE cc_start: 0.8407 (mm) cc_final: 0.8085 (mm) REVERT: C 947 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7872 (tttp) REVERT: C 1031 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7424 (pt0) REVERT: H 38 ARG cc_start: 0.4521 (OUTLIER) cc_final: 0.3362 (ttp80) REVERT: L 48 MET cc_start: 0.5141 (OUTLIER) cc_final: 0.4368 (tpp) REVERT: O 30 SER cc_start: 0.3953 (OUTLIER) cc_final: 0.3274 (t) outliers start: 145 outliers final: 84 residues processed: 383 average time/residue: 1.0500 time to fit residues: 506.1088 Evaluate side-chains 347 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 249 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 366 optimal weight: 40.0000 chunk 42 optimal weight: 7.9990 chunk 216 optimal weight: 30.0000 chunk 277 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 320 optimal weight: 0.1980 chunk 212 optimal weight: 0.9990 chunk 378 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 230 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 69 HIS B 196 ASN B 703 ASN B1002 GLN B1071 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS H 35 ASN H 55 HIS L 89 GLN M 96 GLN O 81 GLN O 82AASN ** O 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 32395 Z= 0.421 Angle : 0.805 13.382 44093 Z= 0.401 Chirality : 0.055 0.620 5110 Planarity : 0.005 0.064 5636 Dihedral : 8.545 62.513 5514 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.56 % Favored : 92.18 % Rotamer: Outliers : 4.83 % Allowed : 18.73 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3915 helix: 0.40 (0.20), residues: 685 sheet: -0.65 (0.18), residues: 792 loop : -1.73 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 64 HIS 0.007 0.002 HIS A1048 PHE 0.021 0.002 PHE C1121 TYR 0.024 0.002 TYR A1067 ARG 0.011 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 274 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7497 (mtp85) REVERT: A 293 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6650 (pt) REVERT: A 347 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.5937 (t80) REVERT: A 725 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: A 780 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7119 (pp20) REVERT: A 819 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: A 985 ASP cc_start: 0.6195 (OUTLIER) cc_final: 0.5823 (t70) REVERT: A 1113 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7402 (mt0) REVERT: B 314 GLN cc_start: 0.7113 (tt0) cc_final: 0.6896 (tt0) REVERT: B 458 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7753 (mttp) REVERT: B 493 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6371 (mm-40) REVERT: B 606 ASN cc_start: 0.6776 (m-40) cc_final: 0.6568 (m-40) REVERT: B 902 MET cc_start: 0.8080 (tpp) cc_final: 0.7824 (mmm) REVERT: C 54 LEU cc_start: 0.7273 (mm) cc_final: 0.6931 (mm) REVERT: C 455 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7500 (mp) REVERT: C 725 GLU cc_start: 0.7522 (tt0) cc_final: 0.6919 (tt0) REVERT: C 1000 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8206 (mmt90) REVERT: C 1031 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: L 48 MET cc_start: 0.5264 (OUTLIER) cc_final: 0.4504 (tpp) REVERT: O 50 TYR cc_start: 0.3398 (OUTLIER) cc_final: 0.2618 (m-80) REVERT: O 82 MET cc_start: 0.2188 (mmm) cc_final: 0.1559 (mtp) REVERT: P 19 VAL cc_start: -0.0222 (OUTLIER) cc_final: -0.0453 (p) outliers start: 165 outliers final: 95 residues processed: 402 average time/residue: 1.0108 time to fit residues: 515.4969 Evaluate side-chains 355 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 244 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain P residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 234 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 240 optimal weight: 4.9990 chunk 258 optimal weight: 9.9990 chunk 187 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 394 ASN A 655 HIS A1010 GLN B 271 GLN B 703 ASN B1002 GLN B1071 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN H 35 ASN H 55 HIS L 89 GLN M 96 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 32395 Z= 0.212 Angle : 0.699 13.223 44093 Z= 0.346 Chirality : 0.050 0.596 5110 Planarity : 0.005 0.063 5636 Dihedral : 8.082 58.674 5514 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.41 % Favored : 93.36 % Rotamer: Outliers : 3.57 % Allowed : 20.34 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.13), residues: 3915 helix: 0.74 (0.20), residues: 686 sheet: -0.55 (0.18), residues: 780 loop : -1.66 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 64 HIS 0.006 0.001 HIS H 98 PHE 0.019 0.001 PHE H 78 TYR 0.022 0.001 TYR C 351 ARG 0.007 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 273 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6585 (pt) REVERT: A 347 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6014 (t80) REVERT: A 661 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6449 (pm20) REVERT: A 819 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: B 347 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.6484 (t80) REVERT: B 493 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.6352 (mm-40) REVERT: B 515 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: B 606 ASN cc_start: 0.6673 (m-40) cc_final: 0.6462 (m-40) REVERT: B 661 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6180 (pm20) REVERT: B 935 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7419 (tp40) REVERT: C 378 LYS cc_start: 0.7299 (pttt) cc_final: 0.7096 (pttm) REVERT: C 455 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7485 (mp) REVERT: C 577 ARG cc_start: 0.4728 (OUTLIER) cc_final: 0.3826 (tpp-160) REVERT: C 725 GLU cc_start: 0.7435 (tt0) cc_final: 0.6824 (tt0) REVERT: C 778 THR cc_start: 0.9048 (t) cc_final: 0.8689 (m) REVERT: C 1000 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7758 (mmt90) REVERT: C 1031 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: L 48 MET cc_start: 0.5247 (OUTLIER) cc_final: 0.4476 (tpp) REVERT: O 30 SER cc_start: 0.4123 (OUTLIER) cc_final: 0.3388 (t) outliers start: 122 outliers final: 70 residues processed: 363 average time/residue: 1.0339 time to fit residues: 479.1219 Evaluate side-chains 332 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 247 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 344 optimal weight: 20.0000 chunk 362 optimal weight: 30.0000 chunk 331 optimal weight: 7.9990 chunk 352 optimal weight: 0.8980 chunk 212 optimal weight: 0.0870 chunk 153 optimal weight: 20.0000 chunk 277 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 318 optimal weight: 0.1980 chunk 333 optimal weight: 1.9990 chunk 351 optimal weight: 0.1980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 655 HIS A1010 GLN B 703 ASN B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1005 GLN H 35 ASN H 55 HIS H 81 GLN L 89 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 32395 Z= 0.211 Angle : 0.695 14.700 44093 Z= 0.342 Chirality : 0.049 0.589 5110 Planarity : 0.005 0.063 5636 Dihedral : 7.811 59.141 5514 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.56 % Favored : 93.21 % Rotamer: Outliers : 3.04 % Allowed : 21.13 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 3915 helix: 0.77 (0.20), residues: 696 sheet: -0.44 (0.18), residues: 781 loop : -1.64 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP H 47 HIS 0.009 0.001 HIS O 98 PHE 0.018 0.001 PHE H 78 TYR 0.023 0.001 TYR C 351 ARG 0.009 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 267 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6563 (pt) REVERT: A 347 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6023 (t80) REVERT: A 661 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6454 (pm20) REVERT: A 819 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7665 (mt-10) REVERT: B 347 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.6644 (t80) REVERT: B 493 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.6374 (mm-40) REVERT: B 515 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7223 (m-80) REVERT: B 606 ASN cc_start: 0.6571 (m-40) cc_final: 0.6363 (m-40) REVERT: B 661 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6189 (pm20) REVERT: B 935 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7304 (tp40) REVERT: C 455 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7465 (mp) REVERT: C 577 ARG cc_start: 0.4761 (OUTLIER) cc_final: 0.4025 (tpp-160) REVERT: C 725 GLU cc_start: 0.7462 (tt0) cc_final: 0.6874 (tt0) REVERT: C 778 THR cc_start: 0.9041 (t) cc_final: 0.8664 (m) REVERT: C 1000 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7919 (mmt90) REVERT: C 1031 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: L 48 MET cc_start: 0.5224 (OUTLIER) cc_final: 0.4362 (tpp) REVERT: M 82 MET cc_start: 0.2153 (tpt) cc_final: 0.0684 (tpt) REVERT: M 91 TYR cc_start: 0.3225 (m-10) cc_final: 0.2410 (p90) REVERT: O 30 SER cc_start: 0.3988 (OUTLIER) cc_final: 0.3652 (t) outliers start: 104 outliers final: 70 residues processed: 344 average time/residue: 0.9870 time to fit residues: 431.2687 Evaluate side-chains 329 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 244 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 30 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 231 optimal weight: 7.9990 chunk 373 optimal weight: 20.0000 chunk 227 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 259 optimal weight: 1.9990 chunk 391 optimal weight: 30.0000 chunk 360 optimal weight: 0.7980 chunk 311 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 240 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 655 HIS A1010 GLN B 703 ASN B1002 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN L 36 HIS L 89 GLN ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 32395 Z= 0.297 Angle : 0.735 15.614 44093 Z= 0.362 Chirality : 0.051 0.587 5110 Planarity : 0.005 0.061 5636 Dihedral : 7.843 58.393 5514 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.97 % Favored : 92.82 % Rotamer: Outliers : 3.16 % Allowed : 21.19 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 3915 helix: 0.74 (0.20), residues: 686 sheet: -0.52 (0.18), residues: 785 loop : -1.58 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 64 HIS 0.005 0.001 HIS H 98 PHE 0.029 0.002 PHE C 106 TYR 0.024 0.002 TYR C 351 ARG 0.008 0.001 ARG C 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7830 Ramachandran restraints generated. 3915 Oldfield, 0 Emsley, 3915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 258 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7526 (mtp85) REVERT: A 293 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6679 (pt) REVERT: A 347 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6001 (t80) REVERT: A 725 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: A 819 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: B 347 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.6684 (t80) REVERT: B 493 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6324 (mm-40) REVERT: B 515 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: B 661 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6293 (pm20) REVERT: B 902 MET cc_start: 0.8047 (tpp) cc_final: 0.7782 (mmm) REVERT: C 54 LEU cc_start: 0.7346 (mm) cc_final: 0.7026 (mm) REVERT: C 378 LYS cc_start: 0.7335 (pttt) cc_final: 0.7066 (pttm) REVERT: C 455 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7476 (mp) REVERT: C 577 ARG cc_start: 0.4991 (OUTLIER) cc_final: 0.4431 (mmp-170) REVERT: C 725 GLU cc_start: 0.7508 (tt0) cc_final: 0.6900 (tt0) REVERT: C 1000 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8125 (mpt-90) REVERT: C 1031 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7477 (pt0) REVERT: L 48 MET cc_start: 0.5266 (OUTLIER) cc_final: 0.4481 (tpp) REVERT: M 82 MET cc_start: 0.1749 (tpt) cc_final: 0.0460 (tpt) outliers start: 108 outliers final: 75 residues processed: 344 average time/residue: 1.0647 time to fit residues: 462.8157 Evaluate side-chains 335 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 246 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain O residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 247 optimal weight: 0.9980 chunk 332 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 287 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 312 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 613 GLN B 703 ASN B1002 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN L 89 GLN ** P 54BHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.227384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.180105 restraints weight = 39964.464| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.46 r_work: 0.3640 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32395 Z= 0.226 Angle : 0.692 14.310 44093 Z= 0.341 Chirality : 0.049 0.579 5110 Planarity : 0.005 0.061 5636 Dihedral : 7.646 59.989 5514 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.51 % Favored : 93.31 % Rotamer: Outliers : 3.07 % Allowed : 21.31 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 3915 helix: 0.80 (0.20), residues: 692 sheet: -0.51 (0.18), residues: 793 loop : -1.55 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 47 HIS 0.006 0.001 HIS A1083 PHE 0.027 0.001 PHE C 106 TYR 0.025 0.001 TYR H 99 ARG 0.007 0.000 ARG C 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9200.48 seconds wall clock time: 165 minutes 53.51 seconds (9953.51 seconds total)