Starting phenix.real_space_refine on Sun Apr 14 23:50:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/04_2024/7n8h_24236.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/04_2024/7n8h_24236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/04_2024/7n8h_24236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/04_2024/7n8h_24236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/04_2024/7n8h_24236.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/04_2024/7n8h_24236.pdb" } resolution = 2.3 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= 0.004 sd= 0.107 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 144 5.16 5 C 20319 2.51 5 N 5382 2.21 5 O 7076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 237": "NH1" <-> "NH2" Residue "F PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "F ARG 408": "NH1" <-> "NH2" Residue "F GLU 773": "OE1" <-> "OE2" Residue "F GLU 780": "OE1" <-> "OE2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 237": "NH1" <-> "NH2" Residue "K PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 273": "NH1" <-> "NH2" Residue "K ARG 408": "NH1" <-> "NH2" Residue "K GLU 773": "OE1" <-> "OE2" Residue "K GLU 780": "OE1" <-> "OE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "M TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 32921 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 7603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7603 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 751 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 538 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 180 Chain: "C" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 596 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 237 Chain: "F" Number of atoms: 7603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7603 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "G" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 751 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 538 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 180 Chain: "J" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 596 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 237 Chain: "K" Number of atoms: 7603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7603 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "L" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 751 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 538 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 180 Chain: "O" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 596 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 237 Chain: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "K" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 181 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 13 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 240 Classifications: {'water': 240} Link IDs: {None: 239} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 240 Classifications: {'water': 240} Link IDs: {None: 239} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "K" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 240 Classifications: {'water': 240} Link IDs: {None: 239} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 18.44, per 1000 atoms: 0.56 Number of scatterers: 32921 At special positions: 0 Unit cell: (144.996, 149.211, 192.204, 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 144 16.00 O 7076 8.00 N 5382 7.00 C 20319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.18 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 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=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.11 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.12 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.14 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.10 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.05 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.02 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.18 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.07 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.01 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.11 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.12 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.04 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.14 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.05 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.02 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.05 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.03 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.02 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.18 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.07 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 488 " distance=2.03 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.01 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.11 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.12 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.03 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.14 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.03 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.10 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.05 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG P 1 " - " FUC P 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG V 1 " - " FUC V 3 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 709 " " NAG A1313 " - " ASN A 282 " " NAG F1301 " - " ASN F 122 " " NAG F1302 " - " ASN F 61 " " NAG F1303 " - " ASN F 234 " " NAG F1304 " - " ASN F 165 " " NAG F1305 " - " ASN F 331 " " NAG F1306 " - " ASN F 603 " " NAG F1307 " - " ASN F 657 " " NAG F1308 " - " ASN F1074 " " NAG F1309 " - " ASN F1098 " " NAG F1310 " - " ASN F1134 " " NAG F1311 " - " ASN F 616 " " NAG F1312 " - " ASN F 709 " " NAG F1313 " - " ASN F 282 " " NAG K1301 " - " ASN K 122 " " NAG K1302 " - " ASN K 61 " " NAG K1303 " - " ASN K 234 " " NAG K1304 " - " ASN K 165 " " NAG K1305 " - " ASN K 331 " " NAG K1308 " - " ASN K 603 " " NAG K1309 " - " ASN K 657 " " NAG K1314 " - " ASN K1074 " " NAG K1315 " - " ASN K1098 " " NAG K1316 " - " ASN K1134 " " NAG K1317 " - " ASN K 616 " " NAG K1318 " - " ASN K 709 " " NAG K1319 " - " ASN K 282 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A 801 " " NAG S 1 " - " ASN F 343 " " NAG T 1 " - " ASN F 717 " " NAG U 1 " - " ASN F 801 " " NAG V 1 " - " ASN K 343 " " NAG W 1 " - " ASN K 717 " " NAG X 1 " - " ASN K 801 " Time building additional restraints: 14.83 Conformation dependent library (CDL) restraints added in 6.2 seconds 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 81 sheets defined 21.1% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.974A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.479A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.737A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.785A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.962A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.066A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.758A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.723A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.610A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 107 through 111 removed outlier: 3.869A pdb=" N TYR E 111 " --> pdb=" O GLY E 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.878A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'F' and resid 383 through 389 removed outlier: 4.974A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.479A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 502 through 505 Processing helix chain 'F' and resid 616 through 620 removed outlier: 3.737A pdb=" N VAL F 620 " --> pdb=" O CYS F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 744 Processing helix chain 'F' and resid 746 through 754 Processing helix chain 'F' and resid 755 through 757 No H-bonds generated for 'chain 'F' and resid 755 through 757' Processing helix chain 'F' and resid 758 through 783 removed outlier: 3.785A pdb=" N ASP F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 824 Processing helix chain 'F' and resid 853 through 856 Processing helix chain 'F' and resid 866 through 885 Processing helix chain 'F' and resid 886 through 891 removed outlier: 3.962A pdb=" N ALA F 890 " --> pdb=" O TRP F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.066A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 939 Processing helix chain 'F' and resid 945 through 965 removed outlier: 3.758A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 984 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 3.723A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.610A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.870A pdb=" N TYR H 111 " --> pdb=" O GLY H 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.878A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 294 through 304 Processing helix chain 'K' and resid 338 through 343 Processing helix chain 'K' and resid 365 through 370 Processing helix chain 'K' and resid 383 through 389 removed outlier: 4.974A pdb=" N ASN K 388 " --> pdb=" O THR K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 removed outlier: 4.479A pdb=" N ARG K 408 " --> pdb=" O ASP K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 422 Processing helix chain 'K' and resid 438 through 443 Processing helix chain 'K' and resid 502 through 505 Processing helix chain 'K' and resid 616 through 620 removed outlier: 3.737A pdb=" N VAL K 620 " --> pdb=" O CYS K 617 " (cutoff:3.500A) Processing helix chain 'K' and resid 737 through 744 Processing helix chain 'K' and resid 746 through 754 Processing helix chain 'K' and resid 755 through 757 No H-bonds generated for 'chain 'K' and resid 755 through 757' Processing helix chain 'K' and resid 758 through 783 removed outlier: 3.785A pdb=" N ASP K 775 " --> pdb=" O ALA K 771 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 824 Processing helix chain 'K' and resid 853 through 856 Processing helix chain 'K' and resid 866 through 885 Processing helix chain 'K' and resid 886 through 891 removed outlier: 3.961A pdb=" N ALA K 890 " --> pdb=" O TRP K 886 " (cutoff:3.500A) Processing helix chain 'K' and resid 897 through 908 Processing helix chain 'K' and resid 912 through 919 removed outlier: 4.065A pdb=" N LEU K 916 " --> pdb=" O THR K 912 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 939 Processing helix chain 'K' and resid 945 through 965 removed outlier: 3.758A pdb=" N VAL K 951 " --> pdb=" O LYS K 947 " (cutoff:3.500A) Processing helix chain 'K' and resid 966 through 968 No H-bonds generated for 'chain 'K' and resid 966 through 968' Processing helix chain 'K' and resid 976 through 984 Processing helix chain 'K' and resid 985 through 1033 removed outlier: 3.723A pdb=" N VAL K 991 " --> pdb=" O PRO K 987 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN K 992 " --> pdb=" O GLU K 988 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.610A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'M' and resid 107 through 111 removed outlier: 3.870A pdb=" N TYR M 111 " --> pdb=" O GLY M 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.877A pdb=" N ILE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.883A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.771A pdb=" N ALA K 575 " --> pdb=" O GLY K 566 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU K 324 " --> pdb=" O ASN K 540 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN K 542 " --> pdb=" O GLU K 324 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE K 326 " --> pdb=" O ASN K 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.425A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.626A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.224A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.294A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE A 565 " --> pdb=" O PHE F 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.701A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.590A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.640A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.640A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.306A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.784A pdb=" N ILE A 788 " --> pdb=" O ASN K 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.612A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 4 through 7 removed outlier: 5.615A pdb=" N THR D 70 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N GLN D 27 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N SER D 68 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N VAL D 29 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N SER D 66 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 54 through 55 removed outlier: 5.582A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 54 through 55 removed outlier: 5.582A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.560A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.560A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR E 114 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.915A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.383A pdb=" N LEU B 33 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.613A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.633A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AD3, first strand: chain 'F' and resid 28 through 31 removed outlier: 3.883A pdb=" N SER F 60 " --> pdb=" O SER F 31 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 47 through 55 removed outlier: 7.425A pdb=" N THR F 274 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP F 290 " --> pdb=" O THR F 274 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU F 276 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA F 288 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS F 278 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.626A pdb=" N VAL F 126 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR F 170 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE F 128 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE F 168 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL F 130 " --> pdb=" O CYS F 166 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N CYS F 166 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER F 162 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 311 through 319 removed outlier: 5.224A pdb=" N ILE F 312 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR F 599 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN F 314 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER F 316 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 324 through 328 removed outlier: 6.293A pdb=" N GLU F 324 " --> pdb=" O ASN F 540 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASN F 542 " --> pdb=" O GLU F 324 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE F 326 " --> pdb=" O ASN F 542 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA F 575 " --> pdb=" O GLY F 566 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE F 565 " --> pdb=" O PHE K 43 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'F' and resid 361 through 362 removed outlier: 6.701A pdb=" N CYS F 361 " --> pdb=" O CYS F 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.590A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 702 through 704 Processing sheet with id=AE5, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.640A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.640A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA F1078 " --> pdb=" O PHE F1095 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.306A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 4.611A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 4 through 7 removed outlier: 5.615A pdb=" N THR G 70 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N GLN G 27 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N SER G 68 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N VAL G 29 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N SER G 66 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 54 through 55 removed outlier: 5.582A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 54 through 55 removed outlier: 5.582A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.560A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.560A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.915A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER I 67 " --> pdb=" O ASP I 70 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.384A pdb=" N LEU I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.613A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.633A pdb=" N MET J 34 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AG3, first strand: chain 'K' and resid 28 through 31 removed outlier: 3.883A pdb=" N SER K 60 " --> pdb=" O SER K 31 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 47 through 55 removed outlier: 7.425A pdb=" N THR K 274 " --> pdb=" O ASP K 290 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP K 290 " --> pdb=" O THR K 274 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU K 276 " --> pdb=" O ALA K 288 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA K 288 " --> pdb=" O LEU K 276 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS K 278 " --> pdb=" O THR K 286 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 84 through 85 removed outlier: 6.626A pdb=" N VAL K 126 " --> pdb=" O TYR K 170 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR K 170 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE K 128 " --> pdb=" O PHE K 168 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE K 168 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL K 130 " --> pdb=" O CYS K 166 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N CYS K 166 " --> pdb=" O VAL K 130 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER K 162 " --> pdb=" O GLN K 134 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 311 through 319 removed outlier: 5.223A pdb=" N ILE K 312 " --> pdb=" O THR K 599 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR K 599 " --> pdb=" O ILE K 312 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN K 314 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL K 597 " --> pdb=" O GLN K 314 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER K 316 " --> pdb=" O VAL K 595 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 354 through 358 Processing sheet with id=AG8, first strand: chain 'K' and resid 361 through 362 removed outlier: 6.701A pdb=" N CYS K 361 " --> pdb=" O CYS K 525 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AH1, first strand: chain 'K' and resid 473 through 474 Processing sheet with id=AH2, first strand: chain 'K' and resid 654 through 655 removed outlier: 6.590A pdb=" N ILE K 670 " --> pdb=" O ILE K 666 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.641A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.641A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA K1078 " --> pdb=" O PHE K1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE K1095 " --> pdb=" O ALA K1078 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 733 through 736 removed outlier: 4.306A pdb=" N LYS K 733 " --> pdb=" O LEU K 861 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 1120 through 1125 removed outlier: 4.611A pdb=" N ALA K1087 " --> pdb=" O SER K1123 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.615A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.582A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 54 through 55 removed outlier: 5.582A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AI2, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.559A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.559A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR M 114 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.915A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER N 67 " --> pdb=" O ASP N 70 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.384A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.614A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AI8, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.633A pdb=" N MET O 34 " --> pdb=" O PHE O 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'O' and resid 10 through 12 1560 hydrogen bonds defined for protein. 3996 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: 21.40 Time building geometry restraints manager: 15.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5784 1.32 - 1.45: 8668 1.45 - 1.57: 18148 1.57 - 1.70: 51 1.70 - 1.83: 186 Bond restraints: 32837 Sorted by residual: bond pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " ideal model delta sigma weight residual 1.439 1.570 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C2 NAG V 1 " pdb=" N2 NAG V 1 " ideal model delta sigma weight residual 1.439 1.570 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" C2 NAG S 1 " pdb=" N2 NAG S 1 " ideal model delta sigma weight residual 1.439 1.570 -0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C4 NAG X 1 " pdb=" O4 NAG X 1 " ideal model delta sigma weight residual 1.409 1.299 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 NAG R 1 " pdb=" O4 NAG R 1 " ideal model delta sigma weight residual 1.409 1.299 0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 32832 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.42: 1030 106.42 - 113.32: 17573 113.32 - 120.23: 11188 120.23 - 127.13: 14922 127.13 - 134.04: 171 Bond angle restraints: 44884 Sorted by residual: angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 126.20 -6.54 7.20e-01 1.93e+00 8.25e+01 angle pdb=" C THR K 791 " pdb=" N PRO K 792 " pdb=" CA PRO K 792 " ideal model delta sigma weight residual 119.66 126.17 -6.51 7.20e-01 1.93e+00 8.18e+01 angle pdb=" C THR F 791 " pdb=" N PRO F 792 " pdb=" CA PRO F 792 " ideal model delta sigma weight residual 119.66 126.16 -6.50 7.20e-01 1.93e+00 8.14e+01 angle pdb=" C LEU K 861 " pdb=" N PRO K 862 " pdb=" CA PRO K 862 " ideal model delta sigma weight residual 119.66 125.55 -5.89 7.20e-01 1.93e+00 6.69e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 125.55 -5.89 7.20e-01 1.93e+00 6.69e+01 ... (remaining 44879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 19369 17.96 - 35.92: 563 35.92 - 53.88: 141 53.88 - 71.85: 48 71.85 - 89.81: 33 Dihedral angle restraints: 20154 sinusoidal: 7593 harmonic: 12561 Sorted by residual: dihedral pdb=" CB CYS O 22 " pdb=" SG CYS O 22 " pdb=" SG CYS O 96 " pdb=" CB CYS O 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.29 41.71 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " pdb=" CB CYS J 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.32 41.68 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.33 41.67 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 20151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4807 0.116 - 0.232: 426 0.232 - 0.347: 74 0.347 - 0.463: 21 0.463 - 0.579: 12 Chirality restraints: 5340 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.95 0.55 2.00e-02 2.50e+03 7.51e+02 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.95 0.55 2.00e-02 2.50e+03 7.45e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.94 0.54 2.00e-02 2.50e+03 7.42e+02 ... (remaining 5337 not shown) Planarity restraints: 5874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " -0.046 2.00e-02 2.50e+03 4.69e-02 2.75e+01 pdb=" CG ASN A 165 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.071 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 165 " 0.046 2.00e-02 2.50e+03 4.68e-02 2.74e+01 pdb=" CG ASN F 165 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN F 165 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN F 165 " -0.071 2.00e-02 2.50e+03 pdb=" C1 NAG F1304 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 165 " -0.046 2.00e-02 2.50e+03 4.67e-02 2.73e+01 pdb=" CG ASN K 165 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN K 165 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN K 165 " 0.071 2.00e-02 2.50e+03 pdb=" C1 NAG K1304 " -0.056 2.00e-02 2.50e+03 ... (remaining 5871 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 13824 2.91 - 3.41: 29272 3.41 - 3.90: 57161 3.90 - 4.40: 64378 4.40 - 4.90: 105121 Nonbonded interactions: 269756 Sorted by model distance: nonbonded pdb=" OE2 GLU K 406 " pdb=" O HOH K1401 " model vdw 2.409 2.440 nonbonded pdb=" OE2 GLU A 406 " pdb=" O HOH A1401 " model vdw 2.409 2.440 nonbonded pdb=" OE2 GLU F 406 " pdb=" O HOH F1401 " model vdw 2.410 2.440 nonbonded pdb=" OD2 ASP K 808 " pdb=" NZ LYS K 811 " model vdw 2.427 2.520 nonbonded pdb=" OD2 ASP F 808 " pdb=" NZ LYS F 811 " model vdw 2.427 2.520 ... (remaining 269751 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 1145 or resid 1301 through 1312 or (resid 1313 \ and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 o \ r name C8 or name N2 or name O3 or name O4 or name O5 or name O6 )))) selection = (chain 'F' and (resid 27 through 1145 or resid 1301 through 1312 or (resid 1313 \ and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 o \ r name C8 or name N2 or name O3 or name O4 or name O5 or name O6 )))) selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'P' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' } 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: 7.230 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: 0.040 Extract box with map and model: 28.690 Check model and map are aligned: 0.520 Set scattering table: 0.330 Process input model: 100.060 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.012 0.131 32837 Z= 0.802 Angle : 1.263 9.964 44884 Z= 0.846 Chirality : 0.083 0.579 5340 Planarity : 0.006 0.035 5826 Dihedral : 10.700 89.808 11937 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.12), residues: 4284 helix: 0.31 (0.19), residues: 669 sheet: 0.95 (0.13), residues: 1368 loop : 0.25 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.005 TRP F 353 HIS 0.004 0.001 HIS A1048 PHE 0.030 0.004 PHE K1075 TYR 0.058 0.006 TYR L 92 ARG 0.033 0.001 ARG F 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 527 time to evaluate : 3.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 ASP cc_start: 0.8051 (t0) cc_final: 0.7823 (t70) REVERT: A 869 MET cc_start: 0.8975 (mtt) cc_final: 0.8399 (mtm) REVERT: A 902 MET cc_start: 0.8669 (tpp) cc_final: 0.8340 (tpp) REVERT: D 4 MET cc_start: 0.5810 (mmm) cc_final: 0.5230 (mmm) REVERT: E 38 ARG cc_start: 0.6353 (ttp-170) cc_final: 0.6137 (ttp-170) REVERT: G 4 MET cc_start: 0.5862 (mmm) cc_final: 0.5550 (mmm) REVERT: K 731 MET cc_start: 0.8236 (mtm) cc_final: 0.7922 (mtm) REVERT: K 902 MET cc_start: 0.8661 (tpp) cc_final: 0.8378 (tpp) REVERT: K 1050 MET cc_start: 0.8842 (ptm) cc_final: 0.8564 (ptm) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 1.3937 time to fit residues: 887.2278 Evaluate side-chains 361 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 3.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 0.9990 chunk 325 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 336 optimal weight: 0.1980 chunk 130 optimal weight: 9.9990 chunk 204 optimal weight: 0.5980 chunk 250 optimal weight: 0.6980 chunk 389 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 544 ASN A 901 GLN A1002 GLN A1058 HIS A1101 HIS F 394 ASN F 564 GLN F 613 GLN F 901 GLN K 564 GLN K 607 GLN K 901 GLN K1058 HIS K1101 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32837 Z= 0.179 Angle : 0.551 6.206 44884 Z= 0.298 Chirality : 0.046 0.160 5340 Planarity : 0.004 0.036 5826 Dihedral : 4.877 34.413 5859 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.69 % Allowed : 5.68 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.12), residues: 4284 helix: 1.96 (0.20), residues: 651 sheet: 1.09 (0.14), residues: 1326 loop : 0.31 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.008 0.002 HIS A1064 PHE 0.013 0.001 PHE A 643 TYR 0.020 0.002 TYR F1067 ARG 0.006 0.001 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 385 time to evaluate : 4.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8918 (mtt) cc_final: 0.8428 (mtm) REVERT: A 902 MET cc_start: 0.8704 (tpp) cc_final: 0.8436 (tpp) REVERT: F 314 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6983 (tt0) REVERT: F 480 CYS cc_start: 0.6096 (m) cc_final: 0.5824 (m) REVERT: G 4 MET cc_start: 0.5882 (mmm) cc_final: 0.5673 (mmm) REVERT: H 46 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6050 (tp30) REVERT: K 479 PRO cc_start: 0.6863 (Cg_exo) cc_final: 0.6609 (Cg_endo) REVERT: K 731 MET cc_start: 0.8266 (mtm) cc_final: 0.7888 (mtm) REVERT: K 780 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7352 (pp20) REVERT: K 820 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7218 (t0) REVERT: K 902 MET cc_start: 0.8709 (tpp) cc_final: 0.8314 (tpp) REVERT: K 1050 MET cc_start: 0.8714 (ptm) cc_final: 0.8288 (ptm) REVERT: M 46 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6027 (tp30) outliers start: 51 outliers final: 25 residues processed: 411 average time/residue: 1.4419 time to fit residues: 713.6043 Evaluate side-chains 381 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 351 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 483 VAL Chi-restraints excluded: chain K residue 780 GLU Chi-restraints excluded: chain K residue 787 GLN Chi-restraints excluded: chain K residue 820 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 56 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 324 optimal weight: 3.9990 chunk 265 optimal weight: 30.0000 chunk 107 optimal weight: 0.9980 chunk 390 optimal weight: 8.9990 chunk 421 optimal weight: 8.9990 chunk 347 optimal weight: 1.9990 chunk 387 optimal weight: 2.9990 chunk 133 optimal weight: 0.0470 chunk 313 optimal weight: 0.3980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 544 ASN A 613 GLN A1101 HIS F 394 ASN F 613 GLN F1002 GLN K 613 GLN K1002 GLN K1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32837 Z= 0.191 Angle : 0.547 7.604 44884 Z= 0.294 Chirality : 0.046 0.197 5340 Planarity : 0.004 0.062 5826 Dihedral : 4.640 30.835 5859 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.16 % Allowed : 6.02 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.12), residues: 4284 helix: 1.86 (0.20), residues: 669 sheet: 1.01 (0.14), residues: 1299 loop : 0.22 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 886 HIS 0.006 0.002 HIS K1064 PHE 0.016 0.002 PHE A 898 TYR 0.021 0.002 TYR F1067 ARG 0.005 0.001 ARG F 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 373 time to evaluate : 3.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.7400 (m-80) cc_final: 0.6937 (m-80) REVERT: A 869 MET cc_start: 0.8931 (mtt) cc_final: 0.8393 (mtm) REVERT: A 902 MET cc_start: 0.8680 (tpp) cc_final: 0.8438 (tpp) REVERT: E 46 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6206 (tp30) REVERT: F 528 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7182 (mttp) REVERT: H 46 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6038 (tp30) REVERT: K 194 PHE cc_start: 0.7402 (m-80) cc_final: 0.6963 (m-80) REVERT: K 567 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6932 (mtt-85) REVERT: K 780 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: K 820 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7204 (t0) REVERT: K 1050 MET cc_start: 0.8757 (ptm) cc_final: 0.8354 (ptm) REVERT: M 46 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6057 (tp30) outliers start: 65 outliers final: 31 residues processed: 413 average time/residue: 1.3664 time to fit residues: 684.2710 Evaluate side-chains 379 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 341 time to evaluate : 3.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 528 LYS Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 567 ARG Chi-restraints excluded: chain K residue 780 GLU Chi-restraints excluded: chain K residue 820 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 262 optimal weight: 0.0970 chunk 391 optimal weight: 0.0970 chunk 414 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 371 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 544 ASN A 613 GLN A 804 GLN A 935 GLN F 394 ASN K1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32837 Z= 0.164 Angle : 0.518 8.171 44884 Z= 0.275 Chirality : 0.045 0.250 5340 Planarity : 0.004 0.038 5826 Dihedral : 4.506 35.001 5859 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.79 % Allowed : 7.28 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 4284 helix: 1.99 (0.20), residues: 669 sheet: 0.91 (0.14), residues: 1347 loop : 0.24 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 50 HIS 0.005 0.001 HIS K1064 PHE 0.014 0.001 PHE K 318 TYR 0.021 0.001 TYR F1067 ARG 0.003 0.000 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 355 time to evaluate : 4.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.7487 (m-80) cc_final: 0.7059 (m-80) REVERT: A 869 MET cc_start: 0.8910 (mtt) cc_final: 0.8371 (mtm) REVERT: A 902 MET cc_start: 0.8674 (tpp) cc_final: 0.8448 (tpp) REVERT: F 528 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7137 (mttp) REVERT: H 46 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.5968 (tp30) REVERT: H 70 MET cc_start: 0.6785 (mtt) cc_final: 0.6529 (mtt) REVERT: K 194 PHE cc_start: 0.7506 (m-80) cc_final: 0.7049 (m-80) REVERT: K 567 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6929 (mtt-85) REVERT: K 780 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7382 (pp20) REVERT: K 820 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7223 (t0) REVERT: K 1050 MET cc_start: 0.8663 (ptm) cc_final: 0.8239 (ptm) outliers start: 54 outliers final: 28 residues processed: 391 average time/residue: 1.4196 time to fit residues: 670.0014 Evaluate side-chains 375 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 342 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 528 LYS Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 567 ARG Chi-restraints excluded: chain K residue 780 GLU Chi-restraints excluded: chain K residue 787 GLN Chi-restraints excluded: chain K residue 820 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 353 optimal weight: 2.9990 chunk 286 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 0.9990 chunk 372 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 544 ASN A 613 GLN E 3 GLN F 394 ASN F 613 GLN ** K 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 32837 Z= 0.360 Angle : 0.693 9.096 44884 Z= 0.370 Chirality : 0.051 0.218 5340 Planarity : 0.005 0.048 5826 Dihedral : 5.474 41.502 5859 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.29 % Allowed : 7.31 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.12), residues: 4284 helix: 1.42 (0.20), residues: 666 sheet: 0.86 (0.14), residues: 1329 loop : -0.05 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP H 50 HIS 0.010 0.002 HIS F1048 PHE 0.021 0.003 PHE A 898 TYR 0.028 0.003 TYR L 92 ARG 0.011 0.001 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 346 time to evaluate : 4.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.8641 (tpp) cc_final: 0.8396 (tpp) REVERT: E 46 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6263 (tp30) REVERT: F 820 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7237 (t0) REVERT: H 46 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6074 (tp30) REVERT: K 194 PHE cc_start: 0.7656 (m-80) cc_final: 0.7319 (m-80) REVERT: K 335 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7925 (mp) REVERT: K 567 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6892 (ttm-80) REVERT: K 613 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7417 (mp10) REVERT: K 780 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7498 (pp20) REVERT: K 820 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7488 (t0) outliers start: 69 outliers final: 37 residues processed: 388 average time/residue: 1.4466 time to fit residues: 672.8013 Evaluate side-chains 378 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 333 time to evaluate : 3.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 820 ASP Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 567 ARG Chi-restraints excluded: chain K residue 613 GLN Chi-restraints excluded: chain K residue 780 GLU Chi-restraints excluded: chain K residue 820 ASP Chi-restraints excluded: chain K residue 826 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 40.0000 chunk 373 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 415 optimal weight: 8.9990 chunk 344 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 544 ASN A 613 GLN E 3 GLN F 394 ASN F 613 GLN K 49 HIS ** K 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 32837 Z= 0.382 Angle : 0.702 9.434 44884 Z= 0.375 Chirality : 0.052 0.293 5340 Planarity : 0.005 0.047 5826 Dihedral : 5.978 51.917 5859 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.29 % Allowed : 7.81 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.12), residues: 4284 helix: 1.31 (0.20), residues: 669 sheet: 0.80 (0.14), residues: 1284 loop : -0.24 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP H 50 HIS 0.011 0.002 HIS F1048 PHE 0.023 0.003 PHE K 759 TYR 0.031 0.003 TYR L 92 ARG 0.010 0.001 ARG F 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 342 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.8643 (tpp) cc_final: 0.8404 (tpp) REVERT: E 46 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6240 (tp30) REVERT: F 820 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7298 (t0) REVERT: H 46 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6219 (tp30) REVERT: K 194 PHE cc_start: 0.7711 (m-80) cc_final: 0.7387 (m-80) REVERT: K 335 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7885 (mp) REVERT: K 567 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6917 (ttm-80) REVERT: K 613 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: K 780 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7382 (pp20) REVERT: K 820 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7466 (t0) REVERT: M 70 MET cc_start: 0.7150 (mtt) cc_final: 0.6857 (mtt) outliers start: 69 outliers final: 43 residues processed: 388 average time/residue: 1.4648 time to fit residues: 684.1722 Evaluate side-chains 381 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 330 time to evaluate : 3.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 820 ASP Chi-restraints excluded: chain F residue 825 LYS Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 367 VAL Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 567 ARG Chi-restraints excluded: chain K residue 613 GLN Chi-restraints excluded: chain K residue 780 GLU Chi-restraints excluded: chain K residue 820 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 75 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 chunk 303 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 349 optimal weight: 0.6980 chunk 231 optimal weight: 0.6980 chunk 413 optimal weight: 20.0000 chunk 258 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 190 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN E 3 GLN F 394 ASN F 613 GLN ** K 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32837 Z= 0.222 Angle : 0.581 8.503 44884 Z= 0.309 Chirality : 0.047 0.213 5340 Planarity : 0.004 0.045 5826 Dihedral : 5.637 56.306 5859 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.96 % Allowed : 8.54 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.12), residues: 4284 helix: 1.61 (0.20), residues: 672 sheet: 0.70 (0.14), residues: 1296 loop : -0.11 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 106 HIS 0.007 0.001 HIS F1048 PHE 0.017 0.002 PHE E 64 TYR 0.022 0.002 TYR G 92 ARG 0.006 0.001 ARG F 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 338 time to evaluate : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.8637 (tpp) cc_final: 0.8396 (tpp) REVERT: E 46 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6249 (tp30) REVERT: F 820 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7148 (t0) REVERT: H 46 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6184 (tp30) REVERT: K 194 PHE cc_start: 0.7674 (m-80) cc_final: 0.7297 (m-80) REVERT: K 335 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7937 (mp) REVERT: K 567 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6872 (ttm-80) REVERT: K 613 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: K 780 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7355 (pp20) outliers start: 59 outliers final: 37 residues processed: 378 average time/residue: 1.4793 time to fit residues: 671.8274 Evaluate side-chains 377 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 333 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 820 ASP Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 567 ARG Chi-restraints excluded: chain K residue 613 GLN Chi-restraints excluded: chain K residue 780 GLU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 262 optimal weight: 0.0980 chunk 281 optimal weight: 7.9990 chunk 204 optimal weight: 0.0870 chunk 38 optimal weight: 0.6980 chunk 325 optimal weight: 4.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN E 3 GLN F 394 ASN F 613 GLN F 804 GLN F 935 GLN K 613 GLN K 804 GLN K 935 GLN K1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32837 Z= 0.129 Angle : 0.493 8.179 44884 Z= 0.259 Chirality : 0.044 0.290 5340 Planarity : 0.004 0.037 5826 Dihedral : 4.938 59.818 5859 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.20 % Allowed : 9.50 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.13), residues: 4284 helix: 1.96 (0.20), residues: 669 sheet: 0.85 (0.14), residues: 1311 loop : 0.06 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 50 HIS 0.004 0.001 HIS K 655 PHE 0.015 0.001 PHE E 64 TYR 0.021 0.001 TYR F1138 ARG 0.006 0.000 ARG D 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 348 time to evaluate : 3.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8868 (mtt) cc_final: 0.8377 (mtm) REVERT: A 902 MET cc_start: 0.8608 (tpp) cc_final: 0.8374 (tpp) REVERT: H 70 MET cc_start: 0.6761 (mtt) cc_final: 0.6438 (mtt) REVERT: K 194 PHE cc_start: 0.7606 (m-80) cc_final: 0.7248 (m-80) outliers start: 36 outliers final: 24 residues processed: 375 average time/residue: 1.3925 time to fit residues: 630.7091 Evaluate side-chains 358 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 334 time to evaluate : 3.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 3.9990 chunk 396 optimal weight: 6.9990 chunk 361 optimal weight: 0.6980 chunk 385 optimal weight: 0.1980 chunk 231 optimal weight: 0.1980 chunk 167 optimal weight: 0.5980 chunk 302 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 348 optimal weight: 1.9990 chunk 364 optimal weight: 3.9990 chunk 383 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 394 ASN E 3 GLN F 394 ASN F 613 GLN K1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32837 Z= 0.169 Angle : 0.530 9.436 44884 Z= 0.279 Chirality : 0.046 0.668 5340 Planarity : 0.004 0.034 5826 Dihedral : 5.051 53.791 5859 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.36 % Allowed : 9.60 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.13), residues: 4284 helix: 1.95 (0.20), residues: 669 sheet: 0.89 (0.14), residues: 1296 loop : 0.05 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 106 HIS 0.005 0.001 HIS K 655 PHE 0.016 0.001 PHE E 64 TYR 0.026 0.002 TYR F1138 ARG 0.005 0.000 ARG D 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 338 time to evaluate : 3.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8900 (mtt) cc_final: 0.8359 (mtm) REVERT: A 902 MET cc_start: 0.8638 (tpp) cc_final: 0.8406 (tpp) REVERT: A 979 ASP cc_start: 0.7530 (m-30) cc_final: 0.6925 (m-30) REVERT: H 46 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6138 (tp30) REVERT: H 70 MET cc_start: 0.6767 (mtt) cc_final: 0.6356 (mtt) REVERT: K 194 PHE cc_start: 0.7607 (m-80) cc_final: 0.7278 (m-80) REVERT: K 528 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7252 (mttp) REVERT: M 70 MET cc_start: 0.6861 (mtt) cc_final: 0.6480 (mtt) outliers start: 41 outliers final: 28 residues processed: 369 average time/residue: 1.4377 time to fit residues: 642.2236 Evaluate side-chains 356 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 326 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 659 SER Chi-restraints excluded: chain F residue 787 GLN Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain K residue 367 VAL Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 10.0000 chunk 407 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 283 optimal weight: 30.0000 chunk 427 optimal weight: 7.9990 chunk 393 optimal weight: 0.3980 chunk 340 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN E 3 GLN F 394 ASN F 613 GLN F1002 GLN K1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32837 Z= 0.227 Angle : 0.580 9.273 44884 Z= 0.307 Chirality : 0.048 0.840 5340 Planarity : 0.004 0.034 5826 Dihedral : 5.367 56.380 5859 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.23 % Allowed : 9.70 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.13), residues: 4284 helix: 1.78 (0.20), residues: 669 sheet: 0.88 (0.14), residues: 1311 loop : 0.01 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 106 HIS 0.006 0.002 HIS F1048 PHE 0.018 0.002 PHE E 64 TYR 0.024 0.002 TYR F1138 ARG 0.005 0.001 ARG F 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 323 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.8643 (tpp) cc_final: 0.8402 (tpp) REVERT: A 979 ASP cc_start: 0.7507 (m-30) cc_final: 0.6866 (m-30) REVERT: H 46 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6171 (tp30) REVERT: H 70 MET cc_start: 0.6889 (mtt) cc_final: 0.6487 (mtt) REVERT: K 194 PHE cc_start: 0.7653 (m-80) cc_final: 0.7323 (m-80) REVERT: K 528 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7342 (mttp) REVERT: K 663 ASP cc_start: 0.7559 (t0) cc_final: 0.7333 (t70) REVERT: M 70 MET cc_start: 0.6885 (mtt) cc_final: 0.6545 (mtt) outliers start: 37 outliers final: 30 residues processed: 354 average time/residue: 1.4995 time to fit residues: 644.1117 Evaluate side-chains 353 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 321 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 659 SER Chi-restraints excluded: chain F residue 994 ASP Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain K residue 367 VAL Chi-restraints excluded: chain K residue 471 GLU Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 820 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 20.0000 chunk 362 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 0.4980 chunk 340 optimal weight: 3.9990 chunk 142 optimal weight: 30.0000 chunk 350 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN D 27 GLN E 3 GLN F 394 ASN F 613 GLN F1002 GLN K1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.208560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.187305 restraints weight = 27747.080| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 0.71 r_work: 0.3914 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 32837 Z= 0.229 Angle : 0.584 8.995 44884 Z= 0.309 Chirality : 0.049 0.707 5340 Planarity : 0.004 0.034 5826 Dihedral : 5.562 57.456 5859 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.26 % Allowed : 9.67 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.79 (0.13), residues: 4284 helix: 1.93 (0.20), residues: 651 sheet: 0.79 (0.14), residues: 1341 loop : 0.01 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 106 HIS 0.006 0.002 HIS F1048 PHE 0.018 0.002 PHE H 64 TYR 0.024 0.002 TYR F1138 ARG 0.005 0.001 ARG F 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11699.93 seconds wall clock time: 210 minutes 54.65 seconds (12654.65 seconds total)