Starting phenix.real_space_refine on Thu Feb 22 15:31:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7so9_25263/02_2024/7so9_25263.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7so9_25263/02_2024/7so9_25263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7so9_25263/02_2024/7so9_25263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7so9_25263/02_2024/7so9_25263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7so9_25263/02_2024/7so9_25263.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7so9_25263/02_2024/7so9_25263.pdb" } resolution = 2.4 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= 0.098 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 168 5.16 5 C 21756 2.51 5 N 5640 2.21 5 O 6906 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 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "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 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 200": "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 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 408": "NH1" <-> "NH2" Residue "F TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 516": "OE1" <-> "OE2" Residue "F PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 737": "OD1" <-> "OD2" Residue "F TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 200": "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 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 408": "NH1" <-> "NH2" Residue "K TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 516": "OE1" <-> "OE2" Residue "K PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 737": "OD1" <-> "OD2" Residue "K TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34470 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7820 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 9 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 749 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 755 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 864 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "F" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7820 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 9 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "G" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 749 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 755 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "J" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 864 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "K" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7820 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 9 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 124 Chain: "L" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 749 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "M" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 755 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "O" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 864 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "F" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "K" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "F" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "K" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Time building chain proxies: 18.21, per 1000 atoms: 0.53 Number of scatterers: 34470 At special positions: 0 Unit cell: (154.269, 152.583, 195.576, 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 168 16.00 O 6906 8.00 N 5640 7.00 C 21756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.17 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.12 Simple disulfide: pdb=" SG CYS A 707 " - pdb=" SG CYS K 883 " distance=2.14 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.10 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS F 707 " distance=2.14 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.17 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=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.04 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=2.17 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 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=2.12 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.10 Simple disulfide: pdb=" SG CYS F 883 " - pdb=" SG CYS K 707 " distance=2.14 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.02 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=2.17 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=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 136 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.03 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=2.17 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.03 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=2.12 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.10 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.02 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=2.17 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=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-6 " NAG P 1 " - " FUC P 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 2 " " NAG R 1 " - " FUC R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A1134 " " NAG A1313 " - " ASN A 616 " " NAG A1314 " - " ASN A 709 " " NAG A1315 " - " ASN A 234 " " NAG F1301 " - " ASN F 61 " " NAG F1302 " - " ASN F 122 " " NAG F1303 " - " ASN F 282 " " NAG F1304 " - " ASN F 165 " " NAG F1305 " - " ASN F 331 " " NAG F1306 " - " ASN F 603 " " NAG F1307 " - " ASN F 657 " " NAG F1308 " - " ASN F 717 " " NAG F1309 " - " ASN F 801 " " NAG F1310 " - " ASN F1074 " " NAG F1311 " - " ASN F1098 " " NAG F1312 " - " ASN F1134 " " NAG F1313 " - " ASN F 616 " " NAG F1314 " - " ASN F 709 " " NAG F1315 " - " ASN F 234 " " NAG K1301 " - " ASN K 61 " " NAG K1302 " - " ASN K 122 " " NAG K1303 " - " ASN K 282 " " NAG K1304 " - " ASN K 165 " " NAG K1305 " - " ASN K 331 " " NAG K1306 " - " ASN K 603 " " NAG K1307 " - " ASN K 657 " " NAG K1308 " - " ASN K 717 " " NAG K1309 " - " ASN K 801 " " NAG K1310 " - " ASN K1074 " " NAG K1311 " - " ASN K1098 " " NAG K1312 " - " ASN K1134 " " NAG K1313 " - " ASN K 616 " " NAG K1314 " - " ASN K 709 " " NAG K1315 " - " ASN K 234 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN F 343 " " NAG R 1 " - " ASN K 343 " Time building additional restraints: 13.60 Conformation dependent library (CDL) restraints added in 6.3 seconds 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 84 sheets defined 19.6% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.250A 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 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: 3.797A 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 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.080A 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: 3.791A 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.525A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (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 'D' and resid 80 through 84 removed outlier: 3.964A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.626A 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: 4.005A pdb=" N TYR E 111 " --> pdb=" O GLY E 108 " (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 303 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'F' and resid 386 through 389 Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.251A 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 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: 3.797A 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 866 through 885 Processing helix chain 'F' and resid 886 through 890 Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.079A 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: 3.791A 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 982 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 3.525A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 995 " --> pdb=" O VAL F 991 " (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 'G' and resid 80 through 84 removed outlier: 3.964A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.626A 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: 4.005A pdb=" N TYR H 111 " --> pdb=" O GLY H 108 " (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 303 Processing helix chain 'K' and resid 338 through 343 Processing helix chain 'K' and resid 365 through 370 Processing helix chain 'K' and resid 386 through 389 Processing helix chain 'K' and resid 405 through 410 removed outlier: 4.250A 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 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: 3.797A 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 866 through 885 Processing helix chain 'K' and resid 886 through 890 Processing helix chain 'K' and resid 897 through 908 Processing helix chain 'K' and resid 912 through 919 removed outlier: 4.079A 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: 3.791A 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 982 Processing helix chain 'K' and resid 985 through 1033 removed outlier: 3.525A pdb=" N VAL K 991 " --> pdb=" O PRO K 987 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG K 995 " --> pdb=" O VAL K 991 " (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 'L' and resid 80 through 84 removed outlier: 3.964A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.626A 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: 4.005A pdb=" N TYR M 111 " --> pdb=" O GLY M 108 " (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 27 through 31 removed outlier: 3.698A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.889A 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: 4.043A pdb=" N ALA F 575 " --> pdb=" O GLY F 566 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU F 324 " --> pdb=" O CYS F 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.633A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.933A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.213A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.004A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.202A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE A 565 " --> pdb=" O PHE K 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.615A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.575A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.709A pdb=" N ALA A 701 " --> pdb=" O ILE K 788 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LYS K 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASN A 703 " --> pdb=" O LYS K 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.373A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.692A pdb=" N LYS A 790 " --> pdb=" O ASN F 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.645A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.534A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.534A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.625A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.625A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR E 114 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.797A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.706A pdb=" N LEU B 11 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 33 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.706A pdb=" N LEU B 11 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.595A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'F' and resid 27 through 31 removed outlier: 3.698A pdb=" N SER F 60 " --> pdb=" O SER F 31 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA F 264 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR F 95 " --> pdb=" O ALA F 264 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS F 187 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 42 through 43 removed outlier: 4.043A pdb=" N ALA K 575 " --> pdb=" O GLY K 566 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU K 324 " --> pdb=" O CYS K 538 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 47 through 55 removed outlier: 7.633A pdb=" N THR F 274 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP F 290 " --> pdb=" O THR F 274 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU F 276 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA F 288 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS F 278 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.213A pdb=" N ALA F 243 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE F 101 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG F 102 " --> pdb=" O ASN F 121 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE F 168 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLU F 132 " --> pdb=" O CYS F 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS F 166 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLN F 134 " --> pdb=" O ASN F 164 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ASN F 164 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 311 through 319 removed outlier: 7.004A pdb=" N VAL F 595 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN F 317 " --> pdb=" O GLY F 593 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY F 593 " --> pdb=" O ASN F 317 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'F' and resid 361 through 362 removed outlier: 6.614A pdb=" N CYS F 361 " --> pdb=" O CYS F 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.574A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA F1078 " --> pdb=" O PHE F1095 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.374A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 787 through 790 removed outlier: 3.692A pdb=" N LYS F 790 " --> pdb=" O ASN K 703 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 4.644A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.533A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.533A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.626A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.626A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.796A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.705A pdb=" N LEU I 11 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.705A pdb=" N LEU I 11 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.594A pdb=" N MET J 34 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AG5, first strand: chain 'K' and resid 27 through 31 removed outlier: 3.698A pdb=" N SER K 60 " --> pdb=" O SER K 31 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA K 264 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR K 95 " --> pdb=" O ALA K 264 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS K 187 " --> pdb=" O ILE K 210 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 47 through 55 removed outlier: 7.633A pdb=" N THR K 274 " --> pdb=" O ASP K 290 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP K 290 " --> pdb=" O THR K 274 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU K 276 " --> pdb=" O ALA K 288 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA K 288 " --> pdb=" O LEU K 276 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS K 278 " --> pdb=" O THR K 286 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 84 through 85 Processing sheet with id=AG8, first strand: chain 'K' and resid 84 through 85 removed outlier: 6.213A pdb=" N ALA K 243 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE K 101 " --> pdb=" O ALA K 243 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG K 102 " --> pdb=" O ASN K 121 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE K 168 " --> pdb=" O VAL K 130 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU K 132 " --> pdb=" O CYS K 166 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS K 166 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN K 134 " --> pdb=" O ASN K 164 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ASN K 164 " --> pdb=" O GLN K 134 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 311 through 319 removed outlier: 7.004A pdb=" N VAL K 595 " --> pdb=" O THR K 315 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN K 317 " --> pdb=" O GLY K 593 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY K 593 " --> pdb=" O ASN K 317 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 354 through 358 Processing sheet with id=AH2, first strand: chain 'K' and resid 361 through 362 removed outlier: 6.614A pdb=" N CYS K 361 " --> pdb=" O CYS K 525 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AH4, first strand: chain 'K' and resid 473 through 474 Processing sheet with id=AH5, first strand: chain 'K' and resid 654 through 655 removed outlier: 6.574A pdb=" N ILE K 670 " --> pdb=" O ILE K 666 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA K1078 " --> pdb=" O PHE K1095 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE K1095 " --> pdb=" O ALA K1078 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 733 through 736 removed outlier: 4.373A pdb=" N LYS K 733 " --> pdb=" O LEU K 861 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 1120 through 1125 removed outlier: 4.644A pdb=" N ALA K1087 " --> pdb=" O SER K1123 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AI2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.534A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.534A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AI5, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.625A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TRP M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.625A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR M 114 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.796A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.706A pdb=" N LEU N 11 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.706A pdb=" N LEU N 11 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AJ2, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.595A pdb=" N MET O 34 " --> pdb=" O PHE O 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 11 through 12 1592 hydrogen bonds defined for protein. 4065 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: 20.33 Time building geometry restraints manager: 14.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5799 1.32 - 1.45: 9687 1.45 - 1.58: 19212 1.58 - 1.71: 0 1.71 - 1.84: 222 Bond restraints: 34920 Sorted by residual: bond pdb=" CA CYS F 15 " pdb=" C CYS F 15 " ideal model delta sigma weight residual 1.524 1.459 0.064 1.30e-02 5.92e+03 2.44e+01 bond pdb=" CA CYS K 15 " pdb=" C CYS K 15 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.30e-02 5.92e+03 2.42e+01 bond pdb=" CA CYS A 15 " pdb=" C CYS A 15 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.30e-02 5.92e+03 2.41e+01 bond pdb=" C GLN F 14 " pdb=" N CYS F 15 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.32e-02 5.74e+03 9.07e+00 bond pdb=" C GLN A 14 " pdb=" N CYS A 15 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.32e-02 5.74e+03 8.93e+00 ... (remaining 34915 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.33: 1059 106.33 - 113.23: 18458 113.23 - 120.13: 11790 120.13 - 127.03: 16070 127.03 - 133.93: 233 Bond angle restraints: 47610 Sorted by residual: angle pdb=" C THR F 791 " pdb=" N PRO F 792 " pdb=" CA PRO F 792 " ideal model delta sigma weight residual 119.66 126.51 -6.85 7.20e-01 1.93e+00 9.05e+01 angle pdb=" C THR K 791 " pdb=" N PRO K 792 " pdb=" CA PRO K 792 " ideal model delta sigma weight residual 119.66 126.50 -6.84 7.20e-01 1.93e+00 9.03e+01 angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.01e+01 angle pdb=" C LEU K 861 " pdb=" N PRO K 862 " pdb=" CA PRO K 862 " ideal model delta sigma weight residual 119.66 126.12 -6.46 7.20e-01 1.93e+00 8.05e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.12 -6.46 7.20e-01 1.93e+00 8.05e+01 ... (remaining 47605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 20394 17.79 - 35.58: 582 35.58 - 53.37: 174 53.37 - 71.17: 51 71.17 - 88.96: 21 Dihedral angle restraints: 21222 sinusoidal: 8397 harmonic: 12825 Sorted by residual: 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 40.52 52.48 1 1.00e+01 1.00e-02 3.75e+01 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 40.52 52.48 1 1.00e+01 1.00e-02 3.75e+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 40.55 52.45 1 1.00e+01 1.00e-02 3.75e+01 ... (remaining 21219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 5415 0.189 - 0.378: 81 0.378 - 0.567: 0 0.567 - 0.756: 0 0.756 - 0.945: 3 Chirality restraints: 5499 Sorted by residual: chirality pdb=" C1 FUC R 2 " pdb=" O6 NAG R 1 " pdb=" C2 FUC R 2 " pdb=" O5 FUC R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.90e+01 chirality pdb=" C1 FUC P 2 " pdb=" O6 NAG P 1 " pdb=" C2 FUC P 2 " pdb=" O5 FUC P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.88e+01 chirality pdb=" C1 FUC Q 2 " pdb=" O6 NAG Q 1 " pdb=" C2 FUC Q 2 " pdb=" O5 FUC Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.79e+01 ... (remaining 5496 not shown) Planarity restraints: 6153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.043 2.00e-02 2.50e+03 4.46e-02 2.49e+01 pdb=" CG ASN A 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 331 " -0.043 2.00e-02 2.50e+03 4.45e-02 2.48e+01 pdb=" CG ASN K 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN K 331 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN K 331 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG K1305 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 331 " -0.043 2.00e-02 2.50e+03 4.44e-02 2.47e+01 pdb=" CG ASN F 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN F 331 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN F 331 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG F1305 " -0.054 2.00e-02 2.50e+03 ... (remaining 6150 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 990 2.70 - 3.25: 32359 3.25 - 3.80: 55640 3.80 - 4.35: 74882 4.35 - 4.90: 121794 Nonbonded interactions: 285665 Sorted by model distance: nonbonded pdb=" O SER H 55 " pdb=" OG SER H 56 " model vdw 2.154 2.440 nonbonded pdb=" O SER E 55 " pdb=" OG SER E 56 " model vdw 2.154 2.440 nonbonded pdb=" O SER M 55 " pdb=" OG SER M 56 " model vdw 2.154 2.440 nonbonded pdb=" O ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.221 3.040 nonbonded pdb=" O ASP G 61 " pdb=" OD1 ASP G 61 " model vdw 2.221 3.040 ... (remaining 285660 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' selection = chain 'F' 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 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 28.590 Check model and map are aligned: 0.660 Set scattering table: 0.400 Process input model: 100.600 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.010 0.064 34920 Z= 0.685 Angle : 1.190 8.388 47610 Z= 0.812 Chirality : 0.069 0.945 5499 Planarity : 0.005 0.023 6105 Dihedral : 10.515 88.957 12843 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.17 % Allowed : 0.79 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.12), residues: 4350 helix: 0.49 (0.19), residues: 657 sheet: 1.05 (0.14), residues: 1299 loop : 0.19 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.005 TRP H 106 HIS 0.004 0.001 HIS K1048 PHE 0.022 0.004 PHE F 898 TYR 0.044 0.005 TYR D 92 ARG 0.004 0.001 ARG K1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 593 time to evaluate : 4.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 TYR cc_start: 0.8137 (t80) cc_final: 0.7897 (t80) REVERT: E 64 PHE cc_start: 0.7042 (m-80) cc_final: 0.6808 (m-80) REVERT: B 9 SER cc_start: 0.7038 (p) cc_final: 0.6768 (t) REVERT: B 54 MET cc_start: 0.6610 (mmm) cc_final: 0.6111 (mmt) REVERT: B 89 GLN cc_start: 0.6955 (tm-30) cc_final: 0.6716 (tm-30) REVERT: I 47 LEU cc_start: 0.7097 (mt) cc_final: 0.6880 (mm) REVERT: I 54 MET cc_start: 0.6519 (mmm) cc_final: 0.6049 (mmt) REVERT: I 86 TYR cc_start: 0.5400 (m-80) cc_final: 0.5017 (m-10) REVERT: I 89 GLN cc_start: 0.6991 (tm-30) cc_final: 0.6630 (tm130) REVERT: K 202 LYS cc_start: 0.6365 (mttt) cc_final: 0.5930 (mmtt) REVERT: N 9 SER cc_start: 0.7237 (p) cc_final: 0.6995 (t) REVERT: O 31 SER cc_start: 0.8344 (p) cc_final: 0.8143 (p) outliers start: 6 outliers final: 0 residues processed: 599 average time/residue: 1.5228 time to fit residues: 1086.5670 Evaluate side-chains 411 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 1.9990 chunk 331 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 343 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 255 optimal weight: 0.9990 chunk 397 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 540 ASN A 755 GLN A 895 GLN D 101 GLN E 117 GLN C 98 ASN F 314 GLN F 564 GLN F 644 GLN F 755 GLN F 804 GLN F 895 GLN F 954 GLN F1005 GLN ** F1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN H 117 GLN I 27 GLN J 98 ASN K 314 GLN K 498 GLN K 540 ASN K 606 ASN K 644 GLN K 755 GLN K 895 GLN K 954 GLN K1005 GLN ** K1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34920 Z= 0.192 Angle : 0.564 8.711 47610 Z= 0.304 Chirality : 0.046 0.494 5499 Planarity : 0.004 0.034 6105 Dihedral : 4.703 36.839 5820 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.77 % Allowed : 7.21 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.12), residues: 4350 helix: 2.09 (0.21), residues: 663 sheet: 1.14 (0.14), residues: 1269 loop : 0.31 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 115 HIS 0.006 0.001 HIS F1064 PHE 0.013 0.002 PHE A 592 TYR 0.021 0.002 TYR F1067 ARG 0.006 0.001 ARG F1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 456 time to evaluate : 4.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.6595 (mttt) cc_final: 0.6037 (mmtt) REVERT: A 586 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7368 (t0) REVERT: B 54 MET cc_start: 0.6740 (mmm) cc_final: 0.6159 (mmt) REVERT: F 202 LYS cc_start: 0.6474 (mttt) cc_final: 0.6071 (mmtt) REVERT: F 586 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7315 (t70) REVERT: G 5 MET cc_start: 0.6107 (tpp) cc_final: 0.5828 (tpp) REVERT: I 47 LEU cc_start: 0.7140 (mt) cc_final: 0.6934 (mm) REVERT: I 54 MET cc_start: 0.6545 (mmm) cc_final: 0.6048 (mmt) REVERT: I 86 TYR cc_start: 0.5574 (m-80) cc_final: 0.5183 (m-10) REVERT: I 89 GLN cc_start: 0.6852 (tm-30) cc_final: 0.6329 (tm130) REVERT: K 202 LYS cc_start: 0.6552 (mttt) cc_final: 0.6163 (mmtt) REVERT: K 207 HIS cc_start: 0.7608 (m-70) cc_final: 0.7361 (m170) REVERT: M 46 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6355 (tp30) REVERT: M 81 MET cc_start: 0.6844 (tmm) cc_final: 0.6621 (tmm) REVERT: N 86 TYR cc_start: 0.5668 (m-80) cc_final: 0.5156 (m-10) REVERT: N 92 ASP cc_start: 0.6279 (t70) cc_final: 0.5869 (t70) outliers start: 61 outliers final: 21 residues processed: 495 average time/residue: 1.4342 time to fit residues: 852.7227 Evaluate side-chains 428 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 404 time to evaluate : 3.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 331 optimal weight: 0.9990 chunk 270 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 398 optimal weight: 2.9990 chunk 430 optimal weight: 6.9990 chunk 354 optimal weight: 0.4980 chunk 395 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 319 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 895 GLN A 954 GLN D 27 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 HIS F 314 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN F 895 GLN F 954 GLN ** F1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN K 498 GLN K 501 ASN K 804 GLN K 872 GLN K 954 GLN ** K1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1113 GLN N 89 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 34920 Z= 0.293 Angle : 0.620 6.975 47610 Z= 0.336 Chirality : 0.048 0.462 5499 Planarity : 0.005 0.036 6105 Dihedral : 4.966 28.408 5820 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.68 % Allowed : 8.17 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.12), residues: 4350 helix: 1.91 (0.20), residues: 666 sheet: 1.04 (0.14), residues: 1263 loop : 0.15 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 36 HIS 0.009 0.002 HIS F1064 PHE 0.027 0.002 PHE A 898 TYR 0.025 0.002 TYR G 92 ARG 0.007 0.001 ARG F 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 414 time to evaluate : 3.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.6758 (mttt) cc_final: 0.6206 (mmtt) REVERT: A 586 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7432 (t0) REVERT: B 54 MET cc_start: 0.6923 (mmm) cc_final: 0.6294 (mmt) REVERT: B 86 TYR cc_start: 0.5690 (m-80) cc_final: 0.5311 (m-10) REVERT: F 48 LEU cc_start: 0.8491 (mt) cc_final: 0.8256 (mp) REVERT: F 202 LYS cc_start: 0.6598 (mttt) cc_final: 0.6248 (mmtt) REVERT: F 554 GLU cc_start: 0.6504 (mm-30) cc_final: 0.6290 (tp30) REVERT: F 586 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7370 (t70) REVERT: F 776 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8608 (tttt) REVERT: H 46 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6391 (tp30) REVERT: I 46 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7122 (tm) REVERT: I 47 LEU cc_start: 0.7082 (mt) cc_final: 0.6739 (mm) REVERT: I 54 MET cc_start: 0.6674 (mmm) cc_final: 0.6102 (mmt) REVERT: I 86 TYR cc_start: 0.5688 (m-80) cc_final: 0.5320 (m-10) REVERT: K 202 LYS cc_start: 0.6515 (mttt) cc_final: 0.6167 (mmtt) REVERT: K 207 HIS cc_start: 0.7726 (m-70) cc_final: 0.7432 (m170) REVERT: M 46 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6392 (tp30) REVERT: M 81 MET cc_start: 0.6929 (tmm) cc_final: 0.6726 (tmm) REVERT: N 4 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.4783 (tpt) REVERT: N 9 SER cc_start: 0.6910 (t) cc_final: 0.6459 (p) REVERT: N 86 TYR cc_start: 0.5863 (m-80) cc_final: 0.5364 (m-10) REVERT: O 96 CYS cc_start: 0.6524 (p) cc_final: 0.6148 (p) outliers start: 92 outliers final: 41 residues processed: 466 average time/residue: 1.4591 time to fit residues: 819.9849 Evaluate side-chains 438 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 390 time to evaluate : 4.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 659 SER Chi-restraints excluded: chain F residue 776 LYS Chi-restraints excluded: chain F residue 808 ASP Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 314 GLN Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 0.7980 chunk 299 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 190 optimal weight: 0.0030 chunk 267 optimal weight: 4.9990 chunk 399 optimal weight: 6.9990 chunk 423 optimal weight: 9.9990 chunk 208 optimal weight: 0.1980 chunk 379 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 954 GLN D 101 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN F 895 GLN F 955 ASN F1005 GLN ** F1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN K 314 GLN K 498 GLN K 501 ASN K 540 ASN K 954 GLN K 955 ASN L 27 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 34920 Z= 0.132 Angle : 0.495 6.777 47610 Z= 0.264 Chirality : 0.044 0.461 5499 Planarity : 0.004 0.035 6105 Dihedral : 4.391 29.634 5820 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.72 % Allowed : 9.57 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.12), residues: 4350 helix: 2.27 (0.21), residues: 663 sheet: 1.09 (0.14), residues: 1290 loop : 0.26 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 106 HIS 0.004 0.001 HIS J 35 PHE 0.014 0.001 PHE F 565 TYR 0.017 0.001 TYR F1067 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 424 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.6665 (mttt) cc_final: 0.6207 (mmtt) REVERT: A 586 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7418 (t0) REVERT: B 54 MET cc_start: 0.6848 (mmm) cc_final: 0.6221 (mmt) REVERT: B 86 TYR cc_start: 0.5661 (m-80) cc_final: 0.5293 (m-10) REVERT: F 48 LEU cc_start: 0.8419 (mt) cc_final: 0.8192 (mp) REVERT: F 202 LYS cc_start: 0.6581 (mttt) cc_final: 0.6203 (mmtt) REVERT: F 207 HIS cc_start: 0.7725 (m90) cc_final: 0.7446 (m-70) REVERT: F 586 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7360 (t70) REVERT: G 5 MET cc_start: 0.6115 (tpp) cc_final: 0.5847 (tpp) REVERT: H 46 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6345 (tp30) REVERT: I 47 LEU cc_start: 0.7168 (mt) cc_final: 0.6876 (mm) REVERT: I 54 MET cc_start: 0.6597 (mmm) cc_final: 0.6019 (mmt) REVERT: I 86 TYR cc_start: 0.5647 (m-80) cc_final: 0.5270 (m-10) REVERT: K 202 LYS cc_start: 0.6474 (mttt) cc_final: 0.6126 (mmtt) REVERT: K 207 HIS cc_start: 0.7704 (m-70) cc_final: 0.7461 (m170) REVERT: K 586 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7320 (t0) REVERT: K 895 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7344 (pp30) REVERT: K 1010 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: M 46 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6346 (tp30) REVERT: N 4 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.4594 (tpt) REVERT: N 9 SER cc_start: 0.7029 (t) cc_final: 0.6509 (p) REVERT: N 86 TYR cc_start: 0.5848 (m-80) cc_final: 0.5359 (m-10) REVERT: O 96 CYS cc_start: 0.6460 (p) cc_final: 0.6044 (p) outliers start: 59 outliers final: 25 residues processed: 453 average time/residue: 1.4384 time to fit residues: 782.3510 Evaluate side-chains 421 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 388 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain K residue 1010 GLN Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 315 optimal weight: 0.3980 chunk 174 optimal weight: 2.9990 chunk 361 optimal weight: 4.9990 chunk 292 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 216 optimal weight: 4.9990 chunk 380 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN A 895 GLN A 926 GLN A 954 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN F 501 ASN F 532 ASN F 564 GLN F 613 GLN F 755 GLN F 926 GLN G 27 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN K 498 GLN K 501 ASN K 926 GLN K 954 GLN K 955 ASN ** K1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1101 HIS L 27 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 34920 Z= 0.368 Angle : 0.671 7.314 47610 Z= 0.361 Chirality : 0.050 0.472 5499 Planarity : 0.005 0.040 6105 Dihedral : 5.260 32.840 5820 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.97 % Allowed : 9.25 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.12), residues: 4350 helix: 1.73 (0.20), residues: 666 sheet: 1.11 (0.14), residues: 1284 loop : -0.04 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 353 HIS 0.010 0.002 HIS K1048 PHE 0.032 0.003 PHE A 898 TYR 0.028 0.003 TYR G 92 ARG 0.009 0.001 ARG F 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 397 time to evaluate : 3.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.6752 (mttt) cc_final: 0.6321 (mmtt) REVERT: A 554 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5590 (mp0) REVERT: A 586 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7417 (t0) REVERT: B 54 MET cc_start: 0.6776 (mmm) cc_final: 0.6570 (mmm) REVERT: B 86 TYR cc_start: 0.5738 (m-80) cc_final: 0.5391 (m-10) REVERT: F 202 LYS cc_start: 0.6692 (mttt) cc_final: 0.6248 (mmtt) REVERT: F 546 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7849 (tp) REVERT: F 586 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7431 (t70) REVERT: F 776 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8596 (tttt) REVERT: F 895 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: F 1045 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7799 (ttpt) REVERT: G 5 MET cc_start: 0.6298 (tpp) cc_final: 0.6017 (tpp) REVERT: H 46 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6405 (tp30) REVERT: I 47 LEU cc_start: 0.7142 (mt) cc_final: 0.6736 (mm) REVERT: I 54 MET cc_start: 0.6696 (mmm) cc_final: 0.6053 (mmt) REVERT: I 86 TYR cc_start: 0.5714 (m-80) cc_final: 0.5377 (m-10) REVERT: K 202 LYS cc_start: 0.6563 (mttt) cc_final: 0.6214 (mmtt) REVERT: K 207 HIS cc_start: 0.7751 (m-70) cc_final: 0.7456 (m170) REVERT: K 703 ASN cc_start: 0.6705 (t0) cc_final: 0.6464 (t0) REVERT: K 895 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7267 (pp30) REVERT: K 947 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7477 (ttpt) REVERT: M 38 ARG cc_start: 0.6428 (OUTLIER) cc_final: 0.5295 (ttm170) REVERT: M 46 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6409 (tp30) REVERT: N 4 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5201 (tpt) REVERT: N 9 SER cc_start: 0.7086 (t) cc_final: 0.6534 (p) REVERT: N 86 TYR cc_start: 0.5989 (m-80) cc_final: 0.5518 (m-10) REVERT: O 96 CYS cc_start: 0.6529 (p) cc_final: 0.6176 (p) outliers start: 102 outliers final: 54 residues processed: 463 average time/residue: 1.4455 time to fit residues: 804.6111 Evaluate side-chains 450 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 383 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 659 SER Chi-restraints excluded: chain F residue 776 LYS Chi-restraints excluded: chain F residue 808 ASP Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain K residue 947 LYS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 20.0000 chunk 381 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 423 optimal weight: 9.9990 chunk 351 optimal weight: 0.0020 chunk 196 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 222 optimal weight: 0.5980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 501 ASN A 532 ASN A 540 ASN A 755 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 101 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN F 895 GLN ** F1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN K 498 GLN K 501 ASN K 540 ASN K 755 GLN K 954 GLN ** K 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN N 89 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34920 Z= 0.145 Angle : 0.513 7.521 47610 Z= 0.272 Chirality : 0.045 0.458 5499 Planarity : 0.004 0.036 6105 Dihedral : 4.561 28.995 5820 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.89 % Allowed : 10.47 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.12), residues: 4350 helix: 2.11 (0.21), residues: 666 sheet: 1.11 (0.14), residues: 1296 loop : 0.11 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 106 HIS 0.005 0.001 HIS K1048 PHE 0.016 0.001 PHE A 898 TYR 0.020 0.001 TYR A 396 ARG 0.006 0.000 ARG K1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 400 time to evaluate : 3.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8532 (mt) cc_final: 0.8263 (mp) REVERT: A 202 LYS cc_start: 0.6731 (mttt) cc_final: 0.6289 (mmtt) REVERT: A 586 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7396 (t0) REVERT: B 54 MET cc_start: 0.6717 (mmm) cc_final: 0.6511 (mmm) REVERT: B 86 TYR cc_start: 0.5650 (m-80) cc_final: 0.5322 (m-10) REVERT: F 48 LEU cc_start: 0.8445 (mt) cc_final: 0.8224 (mp) REVERT: F 202 LYS cc_start: 0.6438 (mttt) cc_final: 0.6039 (mmtt) REVERT: F 586 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7388 (t70) REVERT: F 776 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8573 (tttt) REVERT: G 5 MET cc_start: 0.6275 (tpp) cc_final: 0.6006 (tpp) REVERT: H 46 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6410 (tp30) REVERT: I 47 LEU cc_start: 0.7236 (mt) cc_final: 0.6852 (mm) REVERT: I 54 MET cc_start: 0.6623 (mmm) cc_final: 0.5988 (mmt) REVERT: I 86 TYR cc_start: 0.5669 (m-80) cc_final: 0.5323 (m-10) REVERT: K 202 LYS cc_start: 0.6365 (mttt) cc_final: 0.6108 (mmtt) REVERT: K 207 HIS cc_start: 0.7755 (m-70) cc_final: 0.7506 (m170) REVERT: K 703 ASN cc_start: 0.6415 (t0) cc_final: 0.6185 (t0) REVERT: K 895 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7236 (pp30) REVERT: L 46 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7243 (ptt180) REVERT: M 46 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6372 (tp30) REVERT: N 4 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.5256 (tpt) REVERT: N 9 SER cc_start: 0.7069 (t) cc_final: 0.6514 (p) REVERT: N 86 TYR cc_start: 0.5926 (m-80) cc_final: 0.5484 (m-10) REVERT: O 96 CYS cc_start: 0.6568 (p) cc_final: 0.6183 (p) outliers start: 65 outliers final: 29 residues processed: 440 average time/residue: 1.5051 time to fit residues: 795.1747 Evaluate side-chains 427 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 390 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 776 LYS Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 241 optimal weight: 0.9980 chunk 309 optimal weight: 0.0030 chunk 239 optimal weight: 0.7980 chunk 356 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 422 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 501 ASN A 540 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 101 GLN F 501 ASN F 532 ASN F 755 GLN F 895 GLN G 27 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN K 955 ASN ** K1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34920 Z= 0.219 Angle : 0.564 6.728 47610 Z= 0.300 Chirality : 0.046 0.454 5499 Planarity : 0.004 0.036 6105 Dihedral : 4.723 28.811 5820 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.39 % Allowed : 10.15 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.12), residues: 4350 helix: 2.02 (0.20), residues: 666 sheet: 1.10 (0.14), residues: 1296 loop : 0.07 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 106 HIS 0.007 0.001 HIS K1048 PHE 0.023 0.002 PHE A 898 TYR 0.022 0.002 TYR G 92 ARG 0.009 0.001 ARG K1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 393 time to evaluate : 4.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.6742 (mttt) cc_final: 0.6321 (mmtt) REVERT: A 554 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5553 (mp0) REVERT: A 586 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7432 (t0) REVERT: B 54 MET cc_start: 0.6705 (mmm) cc_final: 0.6071 (mmt) REVERT: B 86 TYR cc_start: 0.5720 (m-80) cc_final: 0.5397 (m-10) REVERT: F 48 LEU cc_start: 0.8469 (mt) cc_final: 0.8253 (mp) REVERT: F 202 LYS cc_start: 0.6460 (mttt) cc_final: 0.6073 (mmtt) REVERT: F 586 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7397 (t70) REVERT: F 776 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8587 (tttt) REVERT: F 1045 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7745 (ttpt) REVERT: G 5 MET cc_start: 0.6310 (tpp) cc_final: 0.6034 (tpp) REVERT: H 46 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6433 (tp30) REVERT: I 46 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7130 (tm) REVERT: I 47 LEU cc_start: 0.7176 (mt) cc_final: 0.6771 (mm) REVERT: I 54 MET cc_start: 0.6623 (mmm) cc_final: 0.6003 (mmt) REVERT: I 86 TYR cc_start: 0.5702 (m-80) cc_final: 0.5380 (m-10) REVERT: K 202 LYS cc_start: 0.6379 (mttt) cc_final: 0.6118 (mmtt) REVERT: K 207 HIS cc_start: 0.7813 (m-70) cc_final: 0.7527 (m170) REVERT: K 586 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7402 (t0) REVERT: K 703 ASN cc_start: 0.6539 (t0) cc_final: 0.6257 (t0) REVERT: K 895 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7256 (pp30) REVERT: L 46 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7123 (ptt-90) REVERT: M 46 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6417 (tp30) REVERT: N 4 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.5290 (tpt) REVERT: N 9 SER cc_start: 0.7029 (t) cc_final: 0.6503 (p) REVERT: N 86 TYR cc_start: 0.5978 (m-80) cc_final: 0.5516 (m-10) outliers start: 82 outliers final: 45 residues processed: 442 average time/residue: 1.4900 time to fit residues: 787.2967 Evaluate side-chains 447 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 390 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 776 LYS Chi-restraints excluded: chain F residue 808 ASP Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain F residue 1045 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 599 THR Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 252 optimal weight: 0.0370 chunk 127 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 268 optimal weight: 0.0870 chunk 287 optimal weight: 0.9980 chunk 208 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 331 optimal weight: 0.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 474 GLN A 501 ASN A 540 ASN A 755 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 101 GLN F 501 ASN F 532 ASN F 755 GLN F 895 GLN ** F1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN ** K1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN N 89 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34920 Z= 0.136 Angle : 0.501 7.127 47610 Z= 0.264 Chirality : 0.044 0.447 5499 Planarity : 0.004 0.039 6105 Dihedral : 4.342 28.599 5820 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.04 % Allowed : 10.59 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.12), residues: 4350 helix: 2.19 (0.21), residues: 666 sheet: 1.15 (0.14), residues: 1323 loop : 0.14 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 106 HIS 0.004 0.001 HIS K1048 PHE 0.014 0.001 PHE A 898 TYR 0.017 0.001 TYR K1067 ARG 0.011 0.000 ARG K1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 401 time to evaluate : 4.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8513 (mt) cc_final: 0.8259 (mp) REVERT: A 202 LYS cc_start: 0.6699 (mttt) cc_final: 0.6282 (mmtt) REVERT: A 586 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7433 (t0) REVERT: B 47 LEU cc_start: 0.7088 (mt) cc_final: 0.6839 (mm) REVERT: B 54 MET cc_start: 0.6710 (mmm) cc_final: 0.6101 (mmt) REVERT: B 86 TYR cc_start: 0.5699 (m-80) cc_final: 0.5384 (m-10) REVERT: F 48 LEU cc_start: 0.8413 (mt) cc_final: 0.8189 (mp) REVERT: F 202 LYS cc_start: 0.6441 (mttt) cc_final: 0.6098 (mmtt) REVERT: F 586 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7414 (t0) REVERT: F 776 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8557 (tttt) REVERT: F 895 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: G 5 MET cc_start: 0.6273 (tpp) cc_final: 0.6010 (tpp) REVERT: H 46 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6400 (tp30) REVERT: I 46 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7148 (tm) REVERT: I 47 LEU cc_start: 0.7230 (mt) cc_final: 0.6823 (mm) REVERT: I 54 MET cc_start: 0.6501 (mmm) cc_final: 0.5968 (mmt) REVERT: I 86 TYR cc_start: 0.5647 (m-80) cc_final: 0.5326 (m-10) REVERT: K 202 LYS cc_start: 0.6264 (mttt) cc_final: 0.6049 (mmtt) REVERT: K 207 HIS cc_start: 0.7792 (m-70) cc_final: 0.7533 (m170) REVERT: K 586 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7349 (t0) REVERT: K 703 ASN cc_start: 0.6398 (t0) cc_final: 0.6188 (t0) REVERT: K 895 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7236 (pp30) REVERT: M 46 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6377 (tp30) REVERT: N 4 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5250 (tpt) REVERT: N 9 SER cc_start: 0.7115 (t) cc_final: 0.6600 (p) REVERT: N 86 TYR cc_start: 0.5965 (m-80) cc_final: 0.5520 (m-10) REVERT: O 96 CYS cc_start: 0.6575 (p) cc_final: 0.6269 (p) outliers start: 70 outliers final: 39 residues processed: 446 average time/residue: 1.4794 time to fit residues: 790.1318 Evaluate side-chains 437 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 388 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 659 SER Chi-restraints excluded: chain F residue 776 LYS Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 895 GLN Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 4.9990 chunk 404 optimal weight: 9.9990 chunk 368 optimal weight: 0.4980 chunk 393 optimal weight: 0.0980 chunk 236 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 355 optimal weight: 0.0970 chunk 372 optimal weight: 1.9990 chunk 392 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 501 ASN A 540 ASN A 755 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 101 GLN F 498 GLN F 501 ASN F 532 ASN F 755 GLN F 895 GLN ** F1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN ** K1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1101 HIS L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 34920 Z= 0.136 Angle : 0.499 7.228 47610 Z= 0.262 Chirality : 0.044 0.441 5499 Planarity : 0.004 0.036 6105 Dihedral : 4.232 28.436 5820 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.04 % Allowed : 10.76 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.13), residues: 4350 helix: 2.24 (0.21), residues: 666 sheet: 1.22 (0.14), residues: 1314 loop : 0.18 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 106 HIS 0.004 0.001 HIS K1048 PHE 0.015 0.001 PHE A 898 TYR 0.018 0.001 TYR K1067 ARG 0.007 0.000 ARG F1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 398 time to evaluate : 3.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8508 (mt) cc_final: 0.8253 (mp) REVERT: A 202 LYS cc_start: 0.6688 (mttt) cc_final: 0.6276 (mmtt) REVERT: B 47 LEU cc_start: 0.7010 (mt) cc_final: 0.6741 (mm) REVERT: B 54 MET cc_start: 0.6746 (mmm) cc_final: 0.6123 (mmt) REVERT: B 86 TYR cc_start: 0.5706 (m-80) cc_final: 0.5391 (m-10) REVERT: F 48 LEU cc_start: 0.8382 (mt) cc_final: 0.8158 (mp) REVERT: F 202 LYS cc_start: 0.6364 (mttt) cc_final: 0.6036 (mmtt) REVERT: F 586 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7419 (t0) REVERT: F 895 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7769 (pm20) REVERT: G 5 MET cc_start: 0.6264 (tpp) cc_final: 0.5976 (tpp) REVERT: H 46 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6385 (tp30) REVERT: I 46 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7179 (tm) REVERT: I 47 LEU cc_start: 0.7192 (mt) cc_final: 0.6774 (mm) REVERT: I 54 MET cc_start: 0.6597 (mmm) cc_final: 0.5990 (mmt) REVERT: I 86 TYR cc_start: 0.5660 (m-80) cc_final: 0.5317 (m-10) REVERT: K 202 LYS cc_start: 0.6266 (mttt) cc_final: 0.6043 (mmtt) REVERT: K 207 HIS cc_start: 0.7752 (m-70) cc_final: 0.7516 (m170) REVERT: M 46 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6357 (tp30) REVERT: N 4 MET cc_start: 0.5852 (OUTLIER) cc_final: 0.5179 (tpt) REVERT: N 9 SER cc_start: 0.7129 (t) cc_final: 0.6620 (p) REVERT: N 86 TYR cc_start: 0.5933 (m-80) cc_final: 0.5497 (m-10) outliers start: 70 outliers final: 43 residues processed: 443 average time/residue: 1.5061 time to fit residues: 805.1014 Evaluate side-chains 439 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 390 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 659 SER Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 9.9990 chunk 415 optimal weight: 4.9990 chunk 253 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 289 optimal weight: 1.9990 chunk 436 optimal weight: 8.9990 chunk 401 optimal weight: 0.0570 chunk 347 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 501 ASN A 540 ASN A 755 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 101 GLN F 498 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN F 895 GLN ** F1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN ** K1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1101 HIS L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34920 Z= 0.153 Angle : 0.509 6.944 47610 Z= 0.269 Chirality : 0.045 0.436 5499 Planarity : 0.004 0.036 6105 Dihedral : 4.260 28.383 5820 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.01 % Allowed : 10.94 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.13), residues: 4350 helix: 2.22 (0.21), residues: 666 sheet: 1.20 (0.14), residues: 1341 loop : 0.19 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 106 HIS 0.005 0.001 HIS K1048 PHE 0.017 0.001 PHE A 898 TYR 0.031 0.001 TYR K 396 ARG 0.006 0.000 ARG F1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8700 Ramachandran restraints generated. 4350 Oldfield, 0 Emsley, 4350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 385 time to evaluate : 4.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8511 (mt) cc_final: 0.8236 (mp) REVERT: A 202 LYS cc_start: 0.6695 (mttt) cc_final: 0.6287 (mmtt) REVERT: A 895 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: B 47 LEU cc_start: 0.7014 (mt) cc_final: 0.6747 (mm) REVERT: B 54 MET cc_start: 0.6752 (mmm) cc_final: 0.6130 (mmt) REVERT: B 86 TYR cc_start: 0.5751 (m-80) cc_final: 0.5438 (m-10) REVERT: F 48 LEU cc_start: 0.8396 (mt) cc_final: 0.8169 (mp) REVERT: F 202 LYS cc_start: 0.6374 (mttt) cc_final: 0.6056 (mmtt) REVERT: F 586 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7430 (t0) REVERT: F 895 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: G 5 MET cc_start: 0.6261 (tpp) cc_final: 0.5973 (tpp) REVERT: H 46 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6403 (tp30) REVERT: I 46 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7180 (tm) REVERT: I 47 LEU cc_start: 0.7192 (mt) cc_final: 0.6965 (mm) REVERT: I 54 MET cc_start: 0.6506 (mmm) cc_final: 0.6294 (mmm) REVERT: I 86 TYR cc_start: 0.5638 (m-80) cc_final: 0.5303 (m-10) REVERT: K 202 LYS cc_start: 0.6298 (mttt) cc_final: 0.6057 (mmtt) REVERT: K 207 HIS cc_start: 0.7738 (m-70) cc_final: 0.7506 (m170) REVERT: M 46 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6349 (tp30) REVERT: N 4 MET cc_start: 0.5886 (OUTLIER) cc_final: 0.5336 (tpt) REVERT: N 9 SER cc_start: 0.7089 (t) cc_final: 0.6605 (p) REVERT: N 86 TYR cc_start: 0.5972 (m-80) cc_final: 0.5535 (m-10) outliers start: 69 outliers final: 46 residues processed: 428 average time/residue: 1.4472 time to fit residues: 744.3205 Evaluate side-chains 432 residues out of total 3828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 379 time to evaluate : 3.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 586 ASP Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 659 SER Chi-restraints excluded: chain F residue 814 LYS Chi-restraints excluded: chain F residue 895 GLN Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 1010 GLN Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 445 VAL Chi-restraints excluded: chain K residue 571 ASP Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 707 CYS Chi-restraints excluded: chain K residue 931 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 20.0000 chunk 370 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 320 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 96 optimal weight: 0.0570 chunk 348 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 357 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 501 ASN A 540 ASN A 755 GLN A 895 GLN A 954 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 101 GLN F 498 GLN F 501 ASN F 532 ASN F 564 GLN F 755 GLN F 895 GLN ** F1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN K 498 GLN K 501 ASN K 755 GLN K 954 GLN ** K1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1101 HIS L 27 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.199454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.188861 restraints weight = 29913.283| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 0.39 r_work: 0.3974 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34920 Z= 0.172 Angle : 0.524 6.913 47610 Z= 0.277 Chirality : 0.045 0.433 5499 Planarity : 0.004 0.036 6105 Dihedral : 4.339 28.388 5820 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.09 % Allowed : 10.94 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.13), residues: 4350 helix: 2.16 (0.21), residues: 666 sheet: 1.24 (0.14), residues: 1314 loop : 0.15 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 106 HIS 0.005 0.001 HIS K1048 PHE 0.019 0.001 PHE A 898 TYR 0.037 0.002 TYR K 396 ARG 0.007 0.000 ARG F1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13299.22 seconds wall clock time: 237 minutes 34.79 seconds (14254.79 seconds total)