Starting phenix.real_space_refine (version: 1.21rc1) on Tue Aug 22 12:16:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/08_2023/7n8h_24236.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/08_2023/7n8h_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_24236/08_2023/7n8h_24236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/08_2023/7n8h_24236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/08_2023/7n8h_24236.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8h_24236/08_2023/7n8h_24236.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 20319 2.51 5 N 5382 2.21 5 O 7076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "D ASP 71": "OD1" <-> "OD2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 237": "NH1" <-> "NH2" Residue "F PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "F ARG 408": "NH1" <-> "NH2" Residue "F GLU 773": "OE1" <-> "OE2" Residue "F GLU 780": "OE1" <-> "OE2" Residue "G ASP 71": "OD1" <-> "OD2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 237": "NH1" <-> "NH2" Residue "K PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 273": "NH1" <-> "NH2" Residue "K ARG 408": "NH1" <-> "NH2" Residue "K GLU 773": "OE1" <-> "OE2" Residue "K GLU 780": "OE1" <-> "OE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "M TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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 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 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 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: 17.12, per 1000 atoms: 0.52 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: 12.94 Conformation dependent library (CDL) restraints added in 4.7 seconds 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 81 sheets defined 21.1% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 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: 19.41 Time building geometry restraints manager: 13.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5784 1.32 - 1.45: 8668 1.45 - 1.57: 18148 1.57 - 1.70: 51 1.70 - 1.83: 186 Bond restraints: 32837 Sorted by residual: bond pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " ideal model delta sigma weight residual 1.439 1.570 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C2 NAG V 1 " pdb=" N2 NAG V 1 " ideal model delta sigma weight residual 1.439 1.570 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" C2 NAG S 1 " pdb=" N2 NAG S 1 " ideal model delta sigma weight residual 1.439 1.570 -0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C4 NAG X 1 " pdb=" O4 NAG X 1 " ideal model delta sigma weight residual 1.409 1.299 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 NAG R 1 " pdb=" O4 NAG R 1 " ideal model delta sigma weight residual 1.409 1.299 0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 32832 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.42: 1030 106.42 - 113.32: 17573 113.32 - 120.23: 11188 120.23 - 127.13: 14922 127.13 - 134.04: 171 Bond angle restraints: 44884 Sorted by residual: angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 126.20 -6.54 7.20e-01 1.93e+00 8.25e+01 angle pdb=" C THR K 791 " pdb=" N PRO K 792 " pdb=" CA PRO K 792 " ideal model delta sigma weight residual 119.66 126.17 -6.51 7.20e-01 1.93e+00 8.18e+01 angle pdb=" C THR F 791 " pdb=" N PRO F 792 " pdb=" CA PRO F 792 " ideal model delta sigma weight residual 119.66 126.16 -6.50 7.20e-01 1.93e+00 8.14e+01 angle pdb=" C LEU K 861 " pdb=" N PRO K 862 " pdb=" CA PRO K 862 " ideal model delta sigma weight residual 119.66 125.55 -5.89 7.20e-01 1.93e+00 6.69e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 125.55 -5.89 7.20e-01 1.93e+00 6.69e+01 ... (remaining 44879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 18157 17.96 - 35.92: 527 35.92 - 53.88: 141 53.88 - 71.85: 48 71.85 - 89.81: 33 Dihedral angle restraints: 18906 sinusoidal: 6345 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 18903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4807 0.116 - 0.232: 426 0.232 - 0.347: 74 0.347 - 0.463: 21 0.463 - 0.579: 12 Chirality restraints: 5340 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.95 0.55 2.00e-02 2.50e+03 7.51e+02 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.95 0.55 2.00e-02 2.50e+03 7.45e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.94 0.54 2.00e-02 2.50e+03 7.42e+02 ... (remaining 5337 not shown) Planarity restraints: 5874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " -0.046 2.00e-02 2.50e+03 4.69e-02 2.75e+01 pdb=" CG ASN A 165 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.071 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 165 " 0.046 2.00e-02 2.50e+03 4.68e-02 2.74e+01 pdb=" CG ASN F 165 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN F 165 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN F 165 " -0.071 2.00e-02 2.50e+03 pdb=" C1 NAG F1304 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 165 " -0.046 2.00e-02 2.50e+03 4.67e-02 2.73e+01 pdb=" CG ASN K 165 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN K 165 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN K 165 " 0.071 2.00e-02 2.50e+03 pdb=" C1 NAG K1304 " -0.056 2.00e-02 2.50e+03 ... (remaining 5871 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 13824 2.91 - 3.41: 29272 3.41 - 3.90: 57161 3.90 - 4.40: 64378 4.40 - 4.90: 105121 Nonbonded interactions: 269756 Sorted by model distance: nonbonded pdb=" OE2 GLU K 406 " pdb=" O HOH K1401 " model vdw 2.409 2.440 nonbonded pdb=" OE2 GLU A 406 " pdb=" O HOH A1401 " model vdw 2.409 2.440 nonbonded pdb=" OE2 GLU F 406 " pdb=" O HOH F1401 " model vdw 2.410 2.440 nonbonded pdb=" OD2 ASP K 808 " pdb=" NZ LYS K 811 " model vdw 2.427 2.520 nonbonded pdb=" OD2 ASP F 808 " pdb=" NZ LYS F 811 " model vdw 2.427 2.520 ... (remaining 269751 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 1145 or resid 1301 through 1312 or (resid 1313 \ and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 o \ r name C8 or name N2 or name O3 or name O4 or name O5 or name O6 )))) selection = (chain 'F' and (resid 27 through 1145 or resid 1301 through 1312 or (resid 1313 \ and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 o \ r name C8 or name N2 or name O3 or name O4 or name O5 or name O6 )))) selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'P' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 29.920 Check model and map are aligned: 0.480 Set scattering table: 0.250 Process input model: 89.450 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.131 32837 Z= 0.802 Angle : 1.263 9.964 44884 Z= 0.846 Chirality : 0.083 0.579 5340 Planarity : 0.006 0.035 5826 Dihedral : 11.077 89.808 10689 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 0.00 % 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 : 3.460 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: 1.3712 time to fit residues: 873.5321 Evaluate side-chains 361 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 3.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7630 ------------------------------------------------------------------------------- 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: 0.7621 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 32837 Z= 0.180 Angle : 0.557 7.584 44884 Z= 0.301 Chirality : 0.046 0.196 5340 Planarity : 0.004 0.033 5826 Dihedral : 4.590 24.253 4611 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer Outliers : 1.53 % 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: 1.91 (0.20), residues: 654 sheet: 1.09 (0.14), residues: 1329 loop : 0.31 (0.12), residues: 2301 *********************** 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 434 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 388 time to evaluate : 3.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 22 residues processed: 410 average time/residue: 1.3734 time to fit residues: 679.2030 Evaluate side-chains 373 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 351 time to evaluate : 3.168 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 15 residues processed: 7 average time/residue: 0.7281 time to fit residues: 11.5497 ------------------------------------------------------------------------------- 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: 3.9990 chunk 120 optimal weight: 0.0870 chunk 324 optimal weight: 0.8980 chunk 265 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 chunk 390 optimal weight: 8.9990 chunk 421 optimal weight: 7.9990 chunk 347 optimal weight: 1.9990 chunk 387 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 chunk 313 optimal weight: 0.7980 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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: 0.7656 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 32837 Z= 0.193 Angle : 0.550 7.835 44884 Z= 0.295 Chirality : 0.046 0.195 5340 Planarity : 0.004 0.058 5826 Dihedral : 4.510 24.647 4611 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 2.03 % 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: 1.02 (0.12), residues: 4284 helix: 1.87 (0.20), residues: 669 sheet: 0.96 (0.14), residues: 1332 loop : 0.24 (0.12), residues: 2283 *********************** 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 431 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 370 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 30 residues processed: 411 average time/residue: 1.3969 time to fit residues: 694.7909 Evaluate side-chains 373 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 343 time to evaluate : 3.380 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 23 residues processed: 7 average time/residue: 0.7540 time to fit residues: 12.3405 ------------------------------------------------------------------------------- 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: 0.0470 chunk 293 optimal weight: 0.3980 chunk 202 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 262 optimal weight: 2.9990 chunk 391 optimal weight: 10.0000 chunk 414 optimal weight: 10.0000 chunk 204 optimal weight: 0.7980 chunk 371 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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 F 394 ASN F 564 GLN K1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2232 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= 0.177 Angle : 0.527 8.487 44884 Z= 0.280 Chirality : 0.045 0.174 5340 Planarity : 0.004 0.043 5826 Dihedral : 4.394 24.220 4611 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer Outliers : 1.89 % 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: 0.98 (0.12), residues: 4284 helix: 1.87 (0.20), residues: 669 sheet: 0.90 (0.14), residues: 1347 loop : 0.21 (0.13), residues: 2268 *********************** 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 406 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 349 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 34 residues processed: 391 average time/residue: 1.3961 time to fit residues: 662.7484 Evaluate side-chains 369 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 335 time to evaluate : 3.570 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 26 residues processed: 8 average time/residue: 0.8332 time to fit residues: 13.4981 ------------------------------------------------------------------------------- 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: 3.9990 chunk 171 optimal weight: 4.9990 chunk 353 optimal weight: 2.9990 chunk 286 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 0.9990 chunk 372 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 544 ASN A 613 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.104 32837 Z= 0.395 Angle : 0.720 11.011 44884 Z= 0.383 Chirality : 0.052 0.230 5340 Planarity : 0.005 0.052 5826 Dihedral : 5.089 27.848 4611 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.12), residues: 4284 helix: 1.34 (0.20), residues: 666 sheet: 0.84 (0.14), residues: 1326 loop : -0.11 (0.12), residues: 2292 *********************** 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 417 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 344 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 40 residues processed: 391 average time/residue: 1.4062 time to fit residues: 663.8932 Evaluate side-chains 378 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 338 time to evaluate : 3.427 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 32 residues processed: 8 average time/residue: 0.4767 time to fit residues: 10.6513 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 2.9990 chunk 243 optimal weight: 0.0870 chunk 102 optimal weight: 5.9990 chunk 415 optimal weight: 6.9990 chunk 344 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 217 optimal weight: 0.5980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A1101 HIS E 3 GLN F 394 ASN F1002 GLN K 613 GLN K 804 GLN K 935 GLN K1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 32837 Z= 0.239 Angle : 0.589 11.168 44884 Z= 0.312 Chirality : 0.047 0.267 5340 Planarity : 0.004 0.048 5826 Dihedral : 4.749 25.585 4611 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 0.67 (0.12), residues: 4284 helix: 1.57 (0.20), residues: 672 sheet: 0.78 (0.14), residues: 1302 loop : -0.01 (0.12), residues: 2310 *********************** 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 401 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 351 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 36 residues processed: 391 average time/residue: 1.3649 time to fit residues: 647.3940 Evaluate side-chains 375 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 339 time to evaluate : 3.504 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 1.0798 time to fit residues: 10.2058 ------------------------------------------------------------------------------- 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: 0.0470 chunk 46 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 303 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 349 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 413 optimal weight: 20.0000 chunk 258 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- 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 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1002 GLN K 49 HIS K 613 GLN K1101 HIS L 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 32837 Z= 0.336 Angle : 0.677 11.149 44884 Z= 0.358 Chirality : 0.050 0.369 5340 Planarity : 0.005 0.044 5826 Dihedral : 5.019 27.173 4611 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 2.16 % 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: 0.51 (0.12), residues: 4284 helix: 1.36 (0.20), residues: 672 sheet: 0.80 (0.14), residues: 1254 loop : -0.16 (0.12), residues: 2358 *********************** 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 407 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 342 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 42 residues processed: 387 average time/residue: 1.4331 time to fit residues: 671.5662 Evaluate side-chains 375 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 333 time to evaluate : 3.696 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 34 residues processed: 8 average time/residue: 0.5029 time to fit residues: 11.0986 ------------------------------------------------------------------------------- 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: 4.9990 chunk 165 optimal weight: 0.7980 chunk 246 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 262 optimal weight: 0.6980 chunk 281 optimal weight: 10.0000 chunk 204 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 325 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1002 GLN K1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 32837 Z= 0.165 Angle : 0.535 11.747 44884 Z= 0.280 Chirality : 0.045 0.259 5340 Planarity : 0.004 0.041 5826 Dihedral : 4.497 24.137 4611 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 1.43 % 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: 0.75 (0.13), residues: 4284 helix: 1.76 (0.20), residues: 672 sheet: 0.80 (0.14), residues: 1338 loop : 0.00 (0.13), residues: 2274 *********************** 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 385 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 342 time to evaluate : 3.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 33 residues processed: 378 average time/residue: 1.4006 time to fit residues: 641.1476 Evaluate side-chains 367 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 334 time to evaluate : 3.482 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 31 residues processed: 2 average time/residue: 1.7722 time to fit residues: 8.8537 ------------------------------------------------------------------------------- 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: 2.9990 chunk 396 optimal weight: 0.5980 chunk 361 optimal weight: 0.5980 chunk 385 optimal weight: 3.9990 chunk 231 optimal weight: 0.0970 chunk 167 optimal weight: 0.0370 chunk 302 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 348 optimal weight: 2.9990 chunk 364 optimal weight: 3.9990 chunk 383 optimal weight: 0.3980 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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 804 GLN F 935 GLN F1002 GLN K1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 32837 Z= 0.133 Angle : 0.503 11.432 44884 Z= 0.261 Chirality : 0.045 0.557 5340 Planarity : 0.004 0.038 5826 Dihedral : 4.249 49.693 4611 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.13), residues: 4284 helix: 1.99 (0.20), residues: 669 sheet: 0.89 (0.14), residues: 1299 loop : 0.08 (0.13), residues: 2316 *********************** 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 386 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 346 time to evaluate : 3.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 30 residues processed: 381 average time/residue: 1.3788 time to fit residues: 638.5089 Evaluate side-chains 362 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 332 time to evaluate : 3.360 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 0.9981 time to fit residues: 6.9746 ------------------------------------------------------------------------------- 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: 3.9990 chunk 407 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 283 optimal weight: 6.9990 chunk 427 optimal weight: 9.9990 chunk 393 optimal weight: 0.9980 chunk 340 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 208 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 F1002 GLN K1101 HIS M 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2892 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= 0.213 Angle : 0.578 11.486 44884 Z= 0.302 Chirality : 0.049 0.788 5340 Planarity : 0.004 0.036 5826 Dihedral : 4.508 35.232 4611 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.13), residues: 4284 helix: 1.84 (0.20), residues: 669 sheet: 0.93 (0.14), residues: 1296 loop : 0.03 (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 368 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 332 time to evaluate : 3.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 27 residues processed: 366 average time/residue: 1.3998 time to fit residues: 624.0449 Evaluate side-chains 359 residues out of total 3759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 332 time to evaluate : 3.398 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 4.7981 ------------------------------------------------------------------------------- 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: 3.9990 chunk 104 optimal weight: 1.9990 chunk 313 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 340 optimal weight: 3.9990 chunk 142 optimal weight: 30.0000 chunk 350 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 62 optimal weight: 0.4980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 F1002 GLN K1101 HIS M 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.210392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.190241 restraints weight = 27788.253| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 0.68 r_work: 0.3942 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 32837 Z= 0.189 Angle : 0.560 11.521 44884 Z= 0.293 Chirality : 0.047 0.594 5340 Planarity : 0.004 0.036 5826 Dihedral : 4.478 34.679 4611 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.13), residues: 4284 helix: 1.85 (0.20), residues: 669 sheet: 0.94 (0.14), residues: 1311 loop : 0.05 (0.13), residues: 2304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11286.09 seconds wall clock time: 201 minutes 54.01 seconds (12114.01 seconds total)