Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:38:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/12_2022/7n8h_24236.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/12_2022/7n8h_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_24236/12_2022/7n8h_24236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/12_2022/7n8h_24236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/12_2022/7n8h_24236.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/12_2022/7n8h_24236.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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 Convert atoms to be neutral 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-4807/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: 1 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 chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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: 1 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: 18.49, 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: 13.52 Conformation dependent library (CDL) restraints added in 4.9 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: 2.95 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: 18.65 Time building geometry restraints manager: 14.70 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=" C4 NAG X 1 " pdb=" O4 NAG X 1 " ideal model delta sigma weight residual 1.423 1.299 0.124 1.00e-02 1.00e+04 1.55e+02 bond pdb=" C4 NAG R 1 " pdb=" O4 NAG R 1 " ideal model delta sigma weight residual 1.423 1.299 0.124 1.00e-02 1.00e+04 1.54e+02 bond pdb=" C4 NAG U 1 " pdb=" O4 NAG U 1 " ideal model delta sigma weight residual 1.423 1.299 0.124 1.00e-02 1.00e+04 1.54e+02 bond pdb=" C4 NAG T 1 " pdb=" O4 NAG T 1 " ideal model delta sigma weight residual 1.423 1.302 0.121 1.00e-02 1.00e+04 1.46e+02 bond pdb=" C4 NAG Q 1 " pdb=" O4 NAG Q 1 " ideal model delta sigma weight residual 1.423 1.302 0.121 1.00e-02 1.00e+04 1.46e+02 ... (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=" C2 NAG V 1 " pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 109.64 118.34 -8.70 5.38e-01 3.45e+00 2.61e+02 angle pdb=" C2 NAG S 1 " pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 109.64 118.34 -8.70 5.38e-01 3.45e+00 2.61e+02 angle pdb=" C2 NAG P 1 " pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 109.64 118.33 -8.69 5.38e-01 3.45e+00 2.61e+02 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 ... (remaining 44879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 18526 17.96 - 35.92: 527 35.92 - 53.88: 141 53.88 - 71.85: 48 71.85 - 89.81: 33 Dihedral angle restraints: 19275 sinusoidal: 6714 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 19272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 4888 0.119 - 0.239: 365 0.239 - 0.358: 57 0.358 - 0.478: 18 0.478 - 0.597: 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 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. 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: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 28.770 Check model and map are aligned: 0.500 Convert atoms to be neutral: 0.300 Process input model: 90.430 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 0.124 32837 Z= 0.780 Angle : 1.246 9.964 44884 Z= 0.894 Chirality : 0.081 0.597 5340 Planarity : 0.006 0.035 5826 Dihedral : 11.008 89.808 11058 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 3.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 1.2350 time to fit residues: 797.7078 Evaluate side-chains 361 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 3.611 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8778 ------------------------------------------------------------------------------- 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: 0.7980 chunk 389 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7858 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 0.068 32837 Z= 0.181 Angle : 0.536 6.291 44884 Z= 0.297 Chirality : 0.045 0.202 5340 Planarity : 0.004 0.038 5826 Dihedral : 4.872 24.515 4980 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer Outliers : 1.66 % 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: 1.14 (0.12), residues: 4284 helix: 1.94 (0.20), residues: 651 sheet: 1.08 (0.14), residues: 1326 loop : 0.31 (0.12), residues: 2307 *********************** 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 433 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 383 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 24 residues processed: 410 average time/residue: 1.2667 time to fit residues: 636.8101 Evaluate side-chains 376 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 352 time to evaluate : 3.615 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 6 average time/residue: 0.7094 time to fit residues: 10.3659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 265 optimal weight: 30.0000 chunk 107 optimal weight: 0.7980 chunk 390 optimal weight: 8.9990 chunk 421 optimal weight: 10.0000 chunk 347 optimal weight: 1.9990 chunk 387 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 313 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.7902 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 32837 Z= 0.215 Angle : 0.554 7.594 44884 Z= 0.303 Chirality : 0.046 0.216 5340 Planarity : 0.004 0.033 5826 Dihedral : 4.834 24.964 4980 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 2.13 % 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: 1.01 (0.12), residues: 4284 helix: 1.92 (0.20), residues: 651 sheet: 0.98 (0.14), residues: 1302 loop : 0.21 (0.12), residues: 2331 *********************** 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 442 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 378 time to evaluate : 4.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 38 residues processed: 420 average time/residue: 1.3051 time to fit residues: 673.3348 Evaluate side-chains 389 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 351 time to evaluate : 3.560 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 28 residues processed: 10 average time/residue: 0.8482 time to fit residues: 16.5146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 0.9990 chunk 293 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 186 optimal weight: 0.0980 chunk 262 optimal weight: 0.3980 chunk 391 optimal weight: 9.9990 chunk 414 optimal weight: 9.9990 chunk 204 optimal weight: 0.5980 chunk 371 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 K1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 32837 Z= 0.144 Angle : 0.489 7.851 44884 Z= 0.264 Chirality : 0.044 0.191 5340 Planarity : 0.004 0.034 5826 Dihedral : 4.561 23.314 4980 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 1.79 % 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: 1.04 (0.13), residues: 4284 helix: 2.00 (0.20), residues: 669 sheet: 0.92 (0.14), residues: 1332 loop : 0.24 (0.13), residues: 2283 *********************** 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 412 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 358 time to evaluate : 3.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 35 residues processed: 397 average time/residue: 1.2832 time to fit residues: 625.7102 Evaluate side-chains 375 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 340 time to evaluate : 3.263 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 30 residues processed: 5 average time/residue: 0.8224 time to fit residues: 10.1422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 6 optimal weight: 10.0000 chunk 308 optimal weight: 0.0070 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: 0.6980 chunk 372 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 overall best weight: 1.2402 ------------------------------------------------------------------------------- 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 A1101 HIS E 3 GLN F 394 ASN ** F 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 804 GLN K 935 GLN K1101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 32837 Z= 0.233 Angle : 0.566 8.824 44884 Z= 0.307 Chirality : 0.046 0.231 5340 Planarity : 0.004 0.052 5826 Dihedral : 4.844 25.531 4980 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.99 % 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: 0.87 (0.12), residues: 4284 helix: 1.73 (0.20), residues: 669 sheet: 0.89 (0.14), residues: 1329 loop : 0.12 (0.13), residues: 2286 *********************** 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 401 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 341 time to evaluate : 4.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 38 residues processed: 387 average time/residue: 1.3017 time to fit residues: 614.8762 Evaluate side-chains 369 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 331 time to evaluate : 3.569 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 34 residues processed: 4 average time/residue: 0.3015 time to fit residues: 7.0953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 81 optimal weight: 0.0980 chunk 243 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 415 optimal weight: 7.9990 chunk 344 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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 E 3 GLN F 394 ASN F 613 GLN F1002 GLN K 613 GLN K1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 32837 Z= 0.310 Angle : 0.635 9.755 44884 Z= 0.345 Chirality : 0.049 0.279 5340 Planarity : 0.005 0.044 5826 Dihedral : 5.151 26.832 4980 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 2.09 % 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: 1.45 (0.20), residues: 669 sheet: 0.91 (0.14), residues: 1287 loop : -0.07 (0.12), residues: 2328 *********************** 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: 63 poor density : 348 time to evaluate : 3.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 40 residues processed: 393 average time/residue: 1.3238 time to fit residues: 638.8439 Evaluate side-chains 378 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 338 time to evaluate : 4.018 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 33 residues processed: 7 average time/residue: 0.6086 time to fit residues: 11.6858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 303 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 349 optimal weight: 0.5980 chunk 231 optimal weight: 0.9990 chunk 413 optimal weight: 20.0000 chunk 258 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 613 GLN K1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 32837 Z= 0.181 Angle : 0.528 7.943 44884 Z= 0.285 Chirality : 0.045 0.229 5340 Planarity : 0.004 0.042 5826 Dihedral : 4.778 24.767 4980 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 1.60 % 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: 0.80 (0.13), residues: 4284 helix: 1.75 (0.20), residues: 669 sheet: 0.87 (0.14), residues: 1326 loop : 0.03 (0.13), residues: 2289 *********************** 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 396 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 348 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 32 residues processed: 385 average time/residue: 1.3198 time to fit residues: 624.5679 Evaluate side-chains 369 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 337 time to evaluate : 3.629 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 1.0834 time to fit residues: 7.7982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 chunk 246 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 80 optimal weight: 0.0970 chunk 262 optimal weight: 0.6980 chunk 281 optimal weight: 5.9990 chunk 204 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 325 optimal weight: 0.0870 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 K1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 32837 Z= 0.129 Angle : 0.479 7.654 44884 Z= 0.256 Chirality : 0.043 0.210 5340 Planarity : 0.004 0.039 5826 Dihedral : 4.472 22.209 4980 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 1.26 % 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: 0.99 (0.13), residues: 4284 helix: 1.94 (0.20), residues: 669 sheet: 1.00 (0.14), residues: 1302 loop : 0.15 (0.13), residues: 2313 *********************** 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 392 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 354 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 29 residues processed: 388 average time/residue: 1.2565 time to fit residues: 601.9590 Evaluate side-chains 368 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 339 time to evaluate : 3.565 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 2 average time/residue: 1.7709 time to fit residues: 8.8955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 0.6980 chunk 396 optimal weight: 6.9990 chunk 361 optimal weight: 0.6980 chunk 385 optimal weight: 5.9990 chunk 231 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 302 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 348 optimal weight: 1.9990 chunk 364 optimal weight: 1.9990 chunk 383 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7912 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 32837 Z= 0.210 Angle : 0.548 7.545 44884 Z= 0.295 Chirality : 0.048 1.072 5340 Planarity : 0.004 0.037 5826 Dihedral : 4.739 24.527 4980 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 1.46 % 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: 0.91 (0.13), residues: 4284 helix: 1.83 (0.20), residues: 669 sheet: 0.99 (0.14), residues: 1296 loop : 0.08 (0.13), residues: 2319 *********************** 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 382 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 338 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 31 residues processed: 374 average time/residue: 1.2950 time to fit residues: 596.1755 Evaluate side-chains 369 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 338 time to evaluate : 3.614 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 4.9401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 4.9990 chunk 407 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 283 optimal weight: 20.0000 chunk 427 optimal weight: 7.9990 chunk 393 optimal weight: 0.9980 chunk 340 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 262 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN E 3 GLN F 394 ASN F 613 GLN K1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 32837 Z= 0.221 Angle : 0.555 7.727 44884 Z= 0.299 Chirality : 0.047 0.637 5340 Planarity : 0.004 0.037 5826 Dihedral : 4.840 25.183 4980 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 1.30 % 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: 0.85 (0.13), residues: 4284 helix: 1.74 (0.20), residues: 669 sheet: 0.97 (0.14), residues: 1296 loop : 0.04 (0.13), residues: 2319 ********************** 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 378 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 339 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 32 residues processed: 372 average time/residue: 1.2974 time to fit residues: 597.2622 Evaluate side-chains 363 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 331 time to evaluate : 3.995 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 0.9479 time to fit residues: 7.4287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 104 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 0.4980 chunk 340 optimal weight: 0.0030 chunk 142 optimal weight: 30.0000 chunk 350 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 K1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.210882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.189781 restraints weight = 27949.223| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 0.71 r_work: 0.3948 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 32837 Z= 0.142 Angle : 0.497 7.447 44884 Z= 0.266 Chirality : 0.046 0.901 5340 Planarity : 0.004 0.037 5826 Dihedral : 4.631 51.016 4980 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 1.30 % 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: 1.00 (0.13), residues: 4284 helix: 1.94 (0.20), residues: 669 sheet: 1.04 (0.14), residues: 1302 loop : 0.13 (0.13), residues: 2313 =============================================================================== Job complete usr+sys time: 10734.29 seconds wall clock time: 190 minutes 55.04 seconds (11455.04 seconds total)