Starting phenix.real_space_refine on Thu Feb 22 15:42:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ldd_23283/02_2024/7ldd_23283_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ldd_23283/02_2024/7ldd_23283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ldd_23283/02_2024/7ldd_23283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ldd_23283/02_2024/7ldd_23283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ldd_23283/02_2024/7ldd_23283_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ldd_23283/02_2024/7ldd_23283_neut_updated.pdb" } resolution = 3.4 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= -0.000 sd= 0.017 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 148 5.16 5 Cl 2 4.86 5 C 22160 2.51 5 N 5796 2.21 5 O 6400 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 242": "OD1" <-> "OD2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A ARG 624": "NH1" <-> "NH2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 42": "OD1" <-> "OD2" Residue "B PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 245": "OD1" <-> "OD2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ASP 308": "OD1" <-> "OD2" Residue "B TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ASP 490": "OD1" <-> "OD2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ASP 651": "OD1" <-> "OD2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 242": "OD1" <-> "OD2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 295": "OD1" <-> "OD2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 541": "NH1" <-> "NH2" Residue "C PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 623": "OE1" <-> "OE2" Residue "C ARG 624": "NH1" <-> "NH2" Residue "D PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 42": "OD1" <-> "OD2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 125": "OD1" <-> "OD2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D ASP 165": "OD1" <-> "OD2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D ASP 200": "OD1" <-> "OD2" Residue "D TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 245": "OD1" <-> "OD2" Residue "D ASP 246": "OD1" <-> "OD2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D ASP 490": "OD1" <-> "OD2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ASP 651": "OD1" <-> "OD2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 755": "OE1" <-> "OE2" Residue "D PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34528 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 5868 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 776, 5867 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 190 Conformer: "B" Number of residues, atoms: 776, 5867 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 190 bond proxies already assigned to first conformer: 5999 Chain: "B" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5687 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 250 Chain: "C" Number of atoms: 5868 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 776, 5867 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 190 Conformer: "B" Number of residues, atoms: 776, 5867 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 190 bond proxies already assigned to first conformer: 5999 Chain: "D" Number of atoms: 5687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5687 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 250 Chain: "E" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 974 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "F" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 978 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "G" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1134 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 1, 'TRANS': 160} Chain breaks: 3 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "H" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1134 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 1, 'TRANS': 160} Chain breaks: 3 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "I" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1124 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 584 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 12, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 368 Chain: "J" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1042 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 202} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 636 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 349 Chain: "K" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1059 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 200} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 523 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 7, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 294 Chain: "L" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1124 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 584 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 12, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 368 Chain: "M" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1042 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 202} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 636 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 349 Chain: "N" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1059 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 200} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 797 Unresolved non-hydrogen dihedrals: 523 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 7, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 294 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 100 Unusual residues: {'D10': 1, 'HP6': 2, 'NAG': 2, 'OCT': 1, 'R16': 1, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 92 Unusual residues: {'C14': 1, 'D12': 1, 'DD9': 2, 'NAG': 1, 'OCT': 1, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 100 Unusual residues: {'D10': 1, 'HP6': 2, 'NAG': 2, 'OCT': 1, 'R16': 1, 'ZK1': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 92 Unusual residues: {'C14': 1, 'D12': 1, 'DD9': 2, 'NAG': 1, 'OCT': 1, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'C14': 1, 'D10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'C14': 1, 'D10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 77 Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 1, 'XVD': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 77 Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'OCT': 1, 'XVD': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 22.69, per 1000 atoms: 0.66 Number of scatterers: 34528 At special positions: 0 Unit cell: (124.852, 228.559, 270.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 148 16.00 P 4 15.00 F 18 9.00 O 6400 8.00 N 5796 7.00 C 22160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.04 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 906 " - " ASN A 231 " " NAG A 907 " - " ASN A 239 " " NAG B 902 " - " ASN B 349 " " NAG C 906 " - " ASN C 231 " " NAG C 907 " - " ASN C 239 " " NAG D 907 " - " ASN D 349 " " NAG O 1 " - " ASN A 45 " " NAG P 1 " - " ASN A 345 " " NAG Q 1 " - " ASN B 235 " " NAG R 1 " - " ASN C 45 " " NAG S 1 " - " ASN C 345 " " NAG T 1 " - " ASN D 235 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.11 Conformation dependent library (CDL) restraints added in 9.4 seconds 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 50 sheets defined 35.2% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.70 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 49 through 62 removed outlier: 3.642A pdb=" N LYS A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.837A pdb=" N SER A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.816A pdb=" N ARG A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 176 Processing helix chain 'A' and resid 188 through 201 removed outlier: 3.834A pdb=" N GLY A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 258 Processing helix chain 'A' and resid 271 through 291 Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 519 through 541 Processing helix chain 'A' and resid 570 through 580 Processing helix chain 'A' and resid 592 through 624 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 650 through 657 Processing helix chain 'A' and resid 661 through 671 removed outlier: 3.608A pdb=" N LYS A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET A 666 " --> pdb=" O VAL A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 740 through 751 Processing helix chain 'A' and resid 755 through 763 Processing helix chain 'A' and resid 786 through 811 removed outlier: 5.296A pdb=" N GLY A 790 " --> pdb=" O ASN A 787 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 791 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 797 " --> pdb=" O ILE A 794 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 800 " --> pdb=" O GLY A 797 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 801 " --> pdb=" O GLY A 798 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 809 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 29 Processing helix chain 'B' and resid 49 through 62 removed outlier: 3.844A pdb=" N ARG B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.543A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 247 through 255 removed outlier: 3.585A pdb=" N ARG B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 Processing helix chain 'B' and resid 320 through 328 Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.683A pdb=" N PHE B 531 " --> pdb=" O MET B 527 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 584 Processing helix chain 'B' and resid 596 through 625 removed outlier: 4.288A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 removed outlier: 4.350A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 743 through 755 removed outlier: 4.307A pdb=" N LEU B 748 " --> pdb=" O ASN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 789 through 818 removed outlier: 6.158A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 49 through 62 removed outlier: 3.643A pdb=" N LYS C 62 " --> pdb=" O SER C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 86 removed outlier: 3.838A pdb=" N SER C 81 " --> pdb=" O ASN C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 122 Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.815A pdb=" N ARG C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 Processing helix chain 'C' and resid 188 through 201 removed outlier: 3.834A pdb=" N GLY C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS C 200 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C 201 " --> pdb=" O GLN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 258 Processing helix chain 'C' and resid 271 through 291 Processing helix chain 'C' and resid 316 through 324 Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 458 through 464 Processing helix chain 'C' and resid 479 through 482 No H-bonds generated for 'chain 'C' and resid 479 through 482' Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 519 through 541 Processing helix chain 'C' and resid 569 through 580 removed outlier: 3.933A pdb=" N LEU C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP C 574 " --> pdb=" O PHE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 624 Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 650 through 657 Processing helix chain 'C' and resid 661 through 671 removed outlier: 3.689A pdb=" N LYS C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET C 666 " --> pdb=" O VAL C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 692 Processing helix chain 'C' and resid 702 through 710 Processing helix chain 'C' and resid 740 through 751 Processing helix chain 'C' and resid 754 through 763 Processing helix chain 'C' and resid 772 through 774 No H-bonds generated for 'chain 'C' and resid 772 through 774' Processing helix chain 'C' and resid 785 through 812 removed outlier: 3.570A pdb=" N ALA C 789 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLY C 790 " --> pdb=" O ASN C 787 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 791 " --> pdb=" O VAL C 788 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR C 812 " --> pdb=" O GLU C 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 49 through 62 removed outlier: 3.843A pdb=" N ARG D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 86 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 133 through 135 No H-bonds generated for 'chain 'D' and resid 133 through 135' Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 167 through 181 removed outlier: 3.543A pdb=" N LYS D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 247 through 255 removed outlier: 3.585A pdb=" N ARG D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 Processing helix chain 'D' and resid 320 through 328 Processing helix chain 'D' and resid 424 through 435 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 523 through 546 removed outlier: 3.652A pdb=" N PHE D 531 " --> pdb=" O MET D 527 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 584 Processing helix chain 'D' and resid 596 through 625 removed outlier: 4.167A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 removed outlier: 4.350A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 743 through 755 removed outlier: 4.393A pdb=" N LEU D 748 " --> pdb=" O ASN D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 775 through 778 No H-bonds generated for 'chain 'D' and resid 775 through 778' Processing helix chain 'D' and resid 789 through 818 removed outlier: 6.168A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 36 removed outlier: 3.810A pdb=" N LEU E 14 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 84 removed outlier: 3.931A pdb=" N VAL E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Proline residue: E 70 - end of helix removed outlier: 3.502A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE E 82 " --> pdb=" O PHE E 78 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 107 removed outlier: 3.585A pdb=" N GLY E 92 " --> pdb=" O TRP E 88 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Proline residue: E 96 - end of helix removed outlier: 3.605A pdb=" N HIS E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP E 103 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG E 104 " --> pdb=" O TYR E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 152 removed outlier: 3.902A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE E 146 " --> pdb=" O TYR E 142 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR E 148 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 157 No H-bonds generated for 'chain 'E' and resid 154 through 157' Processing helix chain 'F' and resid 5 through 36 removed outlier: 3.804A pdb=" N LEU F 14 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL F 15 " --> pdb=" O MET F 11 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE F 23 " --> pdb=" O SER F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 84 removed outlier: 3.821A pdb=" N LEU F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Proline residue: F 70 - end of helix removed outlier: 3.566A pdb=" N LEU F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 removed outlier: 3.570A pdb=" N GLY F 92 " --> pdb=" O TRP F 88 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Proline residue: F 96 - end of helix removed outlier: 3.647A pdb=" N HIS F 101 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 104 " --> pdb=" O TYR F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 152 removed outlier: 3.510A pdb=" N LYS F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE F 146 " --> pdb=" O TYR F 142 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 157 No H-bonds generated for 'chain 'F' and resid 154 through 157' Processing helix chain 'G' and resid 22 through 38 removed outlier: 3.651A pdb=" N GLY G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE G 37 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 126 removed outlier: 3.977A pdb=" N VAL G 123 " --> pdb=" O LEU G 120 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL G 124 " --> pdb=" O LEU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 148 removed outlier: 4.311A pdb=" N ALA G 135 " --> pdb=" O PRO G 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA G 146 " --> pdb=" O GLY G 142 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER G 148 " --> pdb=" O CYS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 184 removed outlier: 3.591A pdb=" N ALA G 161 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU G 164 " --> pdb=" O GLY G 160 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL G 166 " --> pdb=" O GLY G 162 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY G 169 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 176 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR G 179 " --> pdb=" O GLY G 175 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA G 182 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 230 removed outlier: 3.555A pdb=" N PHE G 207 " --> pdb=" O TRP G 203 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY G 208 " --> pdb=" O SER G 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY G 209 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE G 212 " --> pdb=" O GLY G 208 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA G 215 " --> pdb=" O SER G 211 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL G 223 " --> pdb=" O GLY G 219 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR G 226 " --> pdb=" O ALA G 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 38 removed outlier: 3.652A pdb=" N GLY H 27 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU H 34 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE H 37 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA H 38 " --> pdb=" O LEU H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 126 removed outlier: 3.978A pdb=" N VAL H 123 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL H 124 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 removed outlier: 4.311A pdb=" N ALA H 135 " --> pdb=" O PRO H 131 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 146 " --> pdb=" O GLY H 142 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER H 148 " --> pdb=" O CYS H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 184 removed outlier: 3.592A pdb=" N ALA H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU H 164 " --> pdb=" O GLY H 160 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL H 166 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY H 169 " --> pdb=" O PHE H 165 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL H 176 " --> pdb=" O ASN H 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR H 179 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA H 182 " --> pdb=" O VAL H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 230 removed outlier: 3.554A pdb=" N PHE H 207 " --> pdb=" O TRP H 203 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY H 209 " --> pdb=" O PHE H 205 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE H 212 " --> pdb=" O GLY H 208 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA H 215 " --> pdb=" O SER H 211 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL H 223 " --> pdb=" O GLY H 219 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE H 225 " --> pdb=" O LEU H 221 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR H 226 " --> pdb=" O ALA H 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 220 No H-bonds generated for 'chain 'I' and resid 218 through 220' Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 151 through 153 No H-bonds generated for 'chain 'J' and resid 151 through 153' Processing helix chain 'J' and resid 184 through 187 No H-bonds generated for 'chain 'J' and resid 184 through 187' Processing helix chain 'K' and resid 64 through 66 No H-bonds generated for 'chain 'K' and resid 64 through 66' Processing helix chain 'K' and resid 161 through 164 Processing helix chain 'L' and resid 218 through 220 No H-bonds generated for 'chain 'L' and resid 218 through 220' Processing helix chain 'M' and resid 123 through 128 Processing helix chain 'M' and resid 151 through 153 No H-bonds generated for 'chain 'M' and resid 151 through 153' Processing helix chain 'M' and resid 184 through 187 No H-bonds generated for 'chain 'M' and resid 184 through 187' Processing helix chain 'N' and resid 64 through 66 No H-bonds generated for 'chain 'N' and resid 64 through 66' Processing helix chain 'N' and resid 161 through 164 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 43 removed outlier: 6.291A pdb=" N ALA A 66 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU A 12 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE A 68 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N CYS A 89 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLY A 69 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE A 91 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 153 through 158 removed outlier: 5.235A pdb=" N LEU A 181 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 235 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 362 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU A 352 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS A 360 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LYS A 354 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 327 through 329 Processing sheet with id= D, first strand: chain 'A' and resid 392 through 395 removed outlier: 6.459A pdb=" N ARG A 437 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N THR A 395 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU A 439 " --> pdb=" O THR A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.293A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 37 through 44 removed outlier: 6.749A pdb=" N ILE B 6 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS B 40 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 8 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ASP B 42 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY B 10 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU B 44 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N PHE B 12 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 153 through 158 removed outlier: 5.093A pdb=" N ARG B 185 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS B 213 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LEU B 188 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE B 215 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASN B 235 " --> pdb=" O TYR B 214 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N ILE B 216 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N SER B 237 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 236 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 366 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU B 356 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS B 364 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS B 358 " --> pdb=" O PRO B 362 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 331 through 334 Processing sheet with id= I, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.708A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 36 through 43 removed outlier: 6.291A pdb=" N ALA C 66 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU C 12 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE C 68 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS C 89 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLY C 69 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE C 91 " --> pdb=" O GLY C 69 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 153 through 158 removed outlier: 5.236A pdb=" N LEU C 181 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE C 235 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 362 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU C 352 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS C 360 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LYS C 354 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE C 358 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 327 through 329 Processing sheet with id= M, first strand: chain 'C' and resid 392 through 395 removed outlier: 6.458A pdb=" N ARG C 437 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N THR C 395 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU C 439 " --> pdb=" O THR C 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.278A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 37 through 44 removed outlier: 6.748A pdb=" N ILE D 6 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS D 40 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE D 8 " --> pdb=" O HIS D 40 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ASP D 42 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY D 10 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU D 44 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N PHE D 12 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 153 through 158 removed outlier: 5.093A pdb=" N ARG D 185 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS D 213 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU D 188 " --> pdb=" O HIS D 213 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE D 215 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASN D 235 " --> pdb=" O TYR D 214 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N ILE D 216 " --> pdb=" O ASN D 235 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N SER D 237 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL D 236 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY D 366 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU D 356 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS D 364 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS D 358 " --> pdb=" O PRO D 362 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 331 through 334 Processing sheet with id= R, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.700A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.631A pdb=" N LYS I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER I 7 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 93 through 97 removed outlier: 5.900A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 68 through 71 Processing sheet with id= V, first strand: chain 'I' and resid 138 through 141 removed outlier: 3.981A pdb=" N ILE I 155 " --> pdb=" O LEU I 211 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU I 211 " --> pdb=" O ILE I 155 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 144 through 147 removed outlier: 6.519A pdb=" N LYS I 241 " --> pdb=" O LEU I 145 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL I 147 " --> pdb=" O LYS I 241 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU I 243 " --> pdb=" O VAL I 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'I' and resid 223 through 227 removed outlier: 3.684A pdb=" N ILE I 186 " --> pdb=" O TRP I 173 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN I 175 " --> pdb=" O LEU I 184 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU I 184 " --> pdb=" O GLN I 175 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 11 through 13 removed outlier: 5.386A pdb=" N LYS J 104 " --> pdb=" O LEU J 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'J' and resid 21 through 25 Processing sheet with id= AA, first strand: chain 'J' and resid 86 through 91 removed outlier: 5.781A pdb=" N GLN J 38 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU J 47 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 133 through 137 Processing sheet with id= AC, first strand: chain 'J' and resid 146 through 150 Processing sheet with id= AD, first strand: chain 'K' and resid 4 through 8 removed outlier: 3.806A pdb=" N LYS K 6 " --> pdb=" O THR K 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR K 24 " --> pdb=" O LYS K 6 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.946A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL K 51 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL K 35 " --> pdb=" O VAL K 51 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL K 109 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 127 through 131 Processing sheet with id= AG, first strand: chain 'K' and resid 158 through 160 Processing sheet with id= AH, first strand: chain 'K' and resid 176 through 178 removed outlier: 4.061A pdb=" N VAL K 176 " --> pdb=" O THR K 183 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR K 183 " --> pdb=" O VAL K 176 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 3 through 7 removed outlier: 3.631A pdb=" N LYS L 3 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER L 7 " --> pdb=" O SER L 21 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER L 21 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 93 through 97 removed outlier: 5.900A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 68 through 71 Processing sheet with id= AL, first strand: chain 'L' and resid 138 through 141 removed outlier: 3.981A pdb=" N ILE L 155 " --> pdb=" O LEU L 211 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU L 211 " --> pdb=" O ILE L 155 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 144 through 147 removed outlier: 6.519A pdb=" N LYS L 241 " --> pdb=" O LEU L 145 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL L 147 " --> pdb=" O LYS L 241 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU L 243 " --> pdb=" O VAL L 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'L' and resid 223 through 227 removed outlier: 3.684A pdb=" N ILE L 186 " --> pdb=" O TRP L 173 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN L 175 " --> pdb=" O LEU L 184 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU L 184 " --> pdb=" O GLN L 175 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'M' and resid 11 through 13 removed outlier: 5.386A pdb=" N LYS M 104 " --> pdb=" O LEU M 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'M' and resid 21 through 25 Processing sheet with id= AQ, first strand: chain 'M' and resid 86 through 91 removed outlier: 5.781A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'M' and resid 133 through 137 Processing sheet with id= AS, first strand: chain 'M' and resid 146 through 150 Processing sheet with id= AT, first strand: chain 'N' and resid 4 through 8 removed outlier: 3.806A pdb=" N LYS N 6 " --> pdb=" O THR N 24 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR N 24 " --> pdb=" O LYS N 6 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.946A pdb=" N TRP N 37 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL N 51 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL N 35 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL N 109 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'N' and resid 127 through 131 Processing sheet with id= AW, first strand: chain 'N' and resid 158 through 160 Processing sheet with id= AX, first strand: chain 'N' and resid 176 through 178 removed outlier: 4.061A pdb=" N VAL N 176 " --> pdb=" O THR N 183 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR N 183 " --> pdb=" O VAL N 176 " (cutoff:3.500A) 1414 hydrogen bonds defined for protein. 3954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.03 Time building geometry restraints manager: 13.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 11362 1.36 - 1.49: 8999 1.49 - 1.62: 14523 1.62 - 1.75: 0 1.75 - 1.88: 234 Bond restraints: 35118 Sorted by residual: bond pdb=" CAU ZK1 C 901 " pdb=" OAB ZK1 C 901 " ideal model delta sigma weight residual 1.215 1.403 -0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" CAU ZK1 B 901 " pdb=" OAB ZK1 B 901 " ideal model delta sigma weight residual 1.215 1.403 -0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" CAU ZK1 A 901 " pdb=" OAB ZK1 A 901 " ideal model delta sigma weight residual 1.215 1.403 -0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" CAU ZK1 D 906 " pdb=" OAB ZK1 D 906 " ideal model delta sigma weight residual 1.215 1.402 -0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" CAT ZK1 C 901 " pdb=" OAA ZK1 C 901 " ideal model delta sigma weight residual 1.214 1.394 -0.180 2.00e-02 2.50e+03 8.13e+01 ... (remaining 35113 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.91: 700 106.91 - 113.69: 19525 113.69 - 120.47: 13138 120.47 - 127.24: 14270 127.24 - 134.02: 270 Bond angle restraints: 47903 Sorted by residual: angle pdb=" N VAL B 159 " pdb=" CA VAL B 159 " pdb=" C VAL B 159 " ideal model delta sigma weight residual 112.29 109.48 2.81 9.40e-01 1.13e+00 8.93e+00 angle pdb=" N VAL D 159 " pdb=" CA VAL D 159 " pdb=" C VAL D 159 " ideal model delta sigma weight residual 112.29 109.50 2.79 9.40e-01 1.13e+00 8.82e+00 angle pdb=" CAM ZK1 B 901 " pdb=" NAX ZK1 B 901 " pdb=" CAN ZK1 B 901 " ideal model delta sigma weight residual 111.06 119.92 -8.86 3.00e+00 1.11e-01 8.72e+00 angle pdb=" CAM ZK1 D 906 " pdb=" NAX ZK1 D 906 " pdb=" CAN ZK1 D 906 " ideal model delta sigma weight residual 111.06 119.89 -8.83 3.00e+00 1.11e-01 8.66e+00 angle pdb=" CAM ZK1 A 901 " pdb=" NAX ZK1 A 901 " pdb=" CAN ZK1 A 901 " ideal model delta sigma weight residual 111.06 119.88 -8.82 3.00e+00 1.11e-01 8.64e+00 ... (remaining 47898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 19792 23.74 - 47.49: 629 47.49 - 71.23: 80 71.23 - 94.97: 42 94.97 - 118.72: 34 Dihedral angle restraints: 20577 sinusoidal: 6243 harmonic: 14334 Sorted by residual: dihedral pdb=" CB CYS G 90 " pdb=" SG CYS G 90 " pdb=" SG CYS G 100 " pdb=" CB CYS G 100 " ideal model delta sinusoidal sigma weight residual -86.00 -27.43 -58.57 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS H 90 " pdb=" SG CYS H 90 " pdb=" SG CYS H 100 " pdb=" CB CYS H 100 " ideal model delta sinusoidal sigma weight residual -86.00 -27.44 -58.56 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual 93.00 131.76 -38.76 1 1.00e+01 1.00e-02 2.11e+01 ... (remaining 20574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 5720 0.256 - 0.511: 2 0.511 - 0.767: 0 0.767 - 1.022: 0 1.022 - 1.278: 2 Chirality restraints: 5724 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-02 2.50e+03 4.08e+03 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-02 2.50e+03 4.08e+03 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.77 0.37 2.00e-02 2.50e+03 3.42e+02 ... (remaining 5721 not shown) Planarity restraints: 6137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 92 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO C 93 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 92 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 93 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 740 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO C 741 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 741 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 741 " 0.015 5.00e-02 4.00e+02 ... (remaining 6134 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1671 2.73 - 3.27: 34706 3.27 - 3.81: 54395 3.81 - 4.36: 61528 4.36 - 4.90: 107440 Nonbonded interactions: 259740 Sorted by model distance: nonbonded pdb=" O4 NAG S 1 " pdb=" O7 NAG S 1 " model vdw 2.187 2.440 nonbonded pdb=" O4 NAG P 1 " pdb=" O7 NAG P 1 " model vdw 2.187 2.440 nonbonded pdb=" OH TYR D 122 " pdb=" OE2 GLU D 356 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR B 122 " pdb=" OE2 GLU B 356 " model vdw 2.199 2.440 nonbonded pdb=" OD2 ASP C 277 " pdb=" OG1 THR C 332 " model vdw 2.215 2.440 ... (remaining 259735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 649 or resid 651 through 813 or resid 901 throug \ h 908)) selection = (chain 'C' and (resid 1 through 649 or resid 651 through 813 or resid 901 throug \ h 908)) } ncs_group { reference = (chain 'B' and (resid 4 through 819 or resid 905)) selection = (chain 'D' and (resid 4 through 819 or (resid 905 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 or name C9 )))) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 2 through 133 or (resid 134 and (name N or name CA or name \ C or name O or name CB )) or resid 135 through 160 or resid 201 through 202)) } ncs_group { reference = (chain 'G' and (resid 19 through 231 or resid 502 or resid 504 through 506)) selection = (chain 'H' and (resid 19 through 231 or resid 502 or resid 504 through 506)) } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.00 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: 10.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 29.650 Check model and map are aligned: 0.650 Set scattering table: 0.330 Process input model: 98.580 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 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 : 0.004 0.188 35118 Z= 0.315 Angle : 0.493 8.859 47903 Z= 0.255 Chirality : 0.047 1.278 5724 Planarity : 0.002 0.033 6125 Dihedral : 13.687 118.717 11331 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.45 % Allowed : 7.19 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % 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: -3.38 (0.10), residues: 4922 helix: -1.53 (0.10), residues: 1862 sheet: -2.42 (0.15), residues: 892 loop : -2.74 (0.11), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 252 HIS 0.002 0.000 HIS C 209 PHE 0.011 0.001 PHE C 127 TYR 0.012 0.001 TYR B 280 ARG 0.001 0.000 ARG D 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 337 time to evaluate : 3.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.6931 (mmm) cc_final: 0.6003 (ttp) REVERT: A 620 LEU cc_start: 0.8023 (mt) cc_final: 0.7468 (mm) REVERT: B 700 TYR cc_start: 0.2799 (t80) cc_final: 0.2290 (t80) REVERT: C 249 MET cc_start: 0.6924 (mmm) cc_final: 0.6030 (ttp) REVERT: D 700 TYR cc_start: 0.2730 (t80) cc_final: 0.2328 (t80) REVERT: F 154 VAL cc_start: 0.6107 (t) cc_final: 0.5832 (p) outliers start: 12 outliers final: 6 residues processed: 349 average time/residue: 0.4489 time to fit residues: 259.1471 Evaluate side-chains 218 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 212 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 257 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 30.0000 chunk 372 optimal weight: 40.0000 chunk 206 optimal weight: 40.0000 chunk 127 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 385 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 287 optimal weight: 9.9990 chunk 446 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 153 GLN A 722 ASN B 18 GLN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 714 GLN C 8 GLN C 19 GLN C 153 GLN C 583 GLN C 722 ASN D 18 GLN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN ** D 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN D 714 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN H 224 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.185 35118 Z= 0.888 Angle : 0.956 14.456 47903 Z= 0.497 Chirality : 0.056 0.371 5724 Planarity : 0.006 0.106 6125 Dihedral : 10.627 103.643 5948 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.87 % Favored : 93.05 % Rotamer: Outliers : 3.15 % Allowed : 14.28 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % 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: -2.82 (0.11), residues: 4922 helix: -0.79 (0.11), residues: 1896 sheet: -2.10 (0.16), residues: 860 loop : -2.74 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 606 HIS 0.014 0.003 HIS C 209 PHE 0.040 0.004 PHE B 50 TYR 0.053 0.003 TYR C 71 ARG 0.017 0.001 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 256 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7740 (tpm-80) REVERT: A 195 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5823 (mp) REVERT: A 252 TRP cc_start: 0.4910 (t60) cc_final: 0.4553 (t60) REVERT: A 281 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8022 (p) REVERT: B 29 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7585 (tp40) REVERT: B 700 TYR cc_start: 0.3605 (t80) cc_final: 0.2751 (t80) REVERT: B 758 LEU cc_start: 0.6941 (mp) cc_final: 0.6731 (tt) REVERT: C 106 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7939 (mm-40) REVERT: C 142 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7746 (tpm-80) REVERT: C 195 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5820 (mp) REVERT: C 252 TRP cc_start: 0.5024 (t60) cc_final: 0.4635 (t60) REVERT: C 281 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.7993 (p) REVERT: C 625 MET cc_start: 0.7382 (ppp) cc_final: 0.7132 (ppp) REVERT: C 670 MET cc_start: 0.5005 (ptm) cc_final: 0.4749 (ttp) REVERT: D 29 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.7528 (tp40) REVERT: D 700 TYR cc_start: 0.3104 (t80) cc_final: 0.2586 (t80) outliers start: 84 outliers final: 56 residues processed: 330 average time/residue: 0.4649 time to fit residues: 257.5172 Evaluate side-chains 292 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 227 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain H residue 91 CYS Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 371 optimal weight: 9.9990 chunk 304 optimal weight: 50.0000 chunk 123 optimal weight: 8.9990 chunk 447 optimal weight: 40.0000 chunk 483 optimal weight: 50.0000 chunk 398 optimal weight: 20.0000 chunk 443 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 359 optimal weight: 5.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 GLN B 208 HIS B 331 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN C 583 GLN D 208 HIS D 331 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.147 35118 Z= 0.695 Angle : 0.824 12.350 47903 Z= 0.424 Chirality : 0.052 0.347 5724 Planarity : 0.005 0.092 6125 Dihedral : 9.907 95.455 5948 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.12 % Allowed : 15.77 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % 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: -2.44 (0.11), residues: 4922 helix: -0.33 (0.12), residues: 1860 sheet: -1.97 (0.17), residues: 852 loop : -2.60 (0.12), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 606 HIS 0.013 0.002 HIS A 209 PHE 0.027 0.003 PHE C 603 TYR 0.045 0.002 TYR A 71 ARG 0.012 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 232 time to evaluate : 3.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7887 (mm-40) REVERT: A 142 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7647 (tpm-80) REVERT: A 249 MET cc_start: 0.6897 (mmm) cc_final: 0.6399 (ttp) REVERT: A 281 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8195 (t) REVERT: A 403 MET cc_start: 0.3187 (mpp) cc_final: 0.2831 (mpp) REVERT: B 29 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7504 (tp40) REVERT: B 106 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.6958 (mp10) REVERT: B 700 TYR cc_start: 0.3428 (t80) cc_final: 0.2618 (t80) REVERT: C 142 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7634 (tpm-80) REVERT: C 249 MET cc_start: 0.6896 (mmm) cc_final: 0.6397 (tmm) REVERT: C 281 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8146 (t) REVERT: C 670 MET cc_start: 0.5051 (OUTLIER) cc_final: 0.4809 (ttp) REVERT: D 29 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7441 (tp40) REVERT: D 106 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.6814 (mp10) REVERT: D 700 TYR cc_start: 0.3321 (t80) cc_final: 0.2616 (t80) REVERT: F 77 LEU cc_start: 0.7515 (tp) cc_final: 0.7183 (pp) outliers start: 110 outliers final: 72 residues processed: 329 average time/residue: 0.4240 time to fit residues: 235.1622 Evaluate side-chains 300 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 218 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 670 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 91 CYS Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 7.9990 chunk 336 optimal weight: 10.0000 chunk 232 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 300 optimal weight: 20.0000 chunk 449 optimal weight: 5.9990 chunk 475 optimal weight: 10.0000 chunk 234 optimal weight: 0.0670 chunk 425 optimal weight: 50.0000 chunk 128 optimal weight: 5.9990 overall best weight: 2.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN B 619 ASN ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 35118 Z= 0.431 Angle : 0.684 14.731 47903 Z= 0.343 Chirality : 0.046 0.313 5724 Planarity : 0.006 0.214 6125 Dihedral : 9.153 89.806 5948 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.52 % Allowed : 17.83 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % 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: -2.12 (0.11), residues: 4922 helix: 0.03 (0.12), residues: 1866 sheet: -1.84 (0.17), residues: 864 loop : -2.52 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 606 HIS 0.006 0.002 HIS C 209 PHE 0.028 0.002 PHE C 603 TYR 0.031 0.002 TYR A 71 ARG 0.010 0.001 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 222 time to evaluate : 4.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7855 (mm-40) REVERT: A 142 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7602 (tpm-80) REVERT: A 249 MET cc_start: 0.6698 (mmm) cc_final: 0.6134 (ttp) REVERT: A 281 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.7993 (t) REVERT: A 403 MET cc_start: 0.3037 (mpp) cc_final: 0.2725 (mpp) REVERT: B 29 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7008 (tp40) REVERT: B 670 MET cc_start: 0.6875 (tmm) cc_final: 0.6546 (ppp) REVERT: B 700 TYR cc_start: 0.2897 (t80) cc_final: 0.2192 (t80) REVERT: C 142 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7636 (tpm-80) REVERT: C 249 MET cc_start: 0.6705 (mmm) cc_final: 0.6158 (ttp) REVERT: C 281 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8024 (t) REVERT: C 403 MET cc_start: 0.3507 (mpp) cc_final: 0.3239 (mpp) REVERT: D 29 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7217 (tp40) outliers start: 94 outliers final: 73 residues processed: 310 average time/residue: 0.4037 time to fit residues: 217.2502 Evaluate side-chains 291 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 211 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 812 TYR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 91 CYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 20.0000 chunk 269 optimal weight: 30.0000 chunk 6 optimal weight: 0.5980 chunk 354 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 405 optimal weight: 50.0000 chunk 328 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 426 optimal weight: 0.7980 chunk 120 optimal weight: 50.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 35118 Z= 0.301 Angle : 0.611 13.953 47903 Z= 0.304 Chirality : 0.044 0.304 5724 Planarity : 0.004 0.120 6125 Dihedral : 8.795 86.525 5948 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.75 % Allowed : 18.40 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % 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: -1.77 (0.12), residues: 4922 helix: 0.38 (0.12), residues: 1846 sheet: -1.72 (0.17), residues: 866 loop : -2.33 (0.12), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 605 HIS 0.005 0.001 HIS C 349 PHE 0.027 0.001 PHE C 603 TYR 0.024 0.001 TYR A 71 ARG 0.005 0.000 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 214 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7776 (mm-40) REVERT: A 142 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7541 (tpm-80) REVERT: A 249 MET cc_start: 0.6624 (mmm) cc_final: 0.6202 (ttp) REVERT: A 252 TRP cc_start: 0.4873 (t60) cc_final: 0.4382 (t60) REVERT: A 281 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.7783 (t) REVERT: A 313 TRP cc_start: 0.7784 (OUTLIER) cc_final: 0.7318 (t60) REVERT: A 325 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7690 (mp10) REVERT: A 403 MET cc_start: 0.2997 (mpp) cc_final: 0.2725 (mpp) REVERT: B 110 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: B 408 MET cc_start: -0.0063 (OUTLIER) cc_final: -0.0313 (mmp) REVERT: B 700 TYR cc_start: 0.2538 (t80) cc_final: 0.2053 (t80) REVERT: C 142 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7531 (tpm-80) REVERT: C 249 MET cc_start: 0.6633 (mmm) cc_final: 0.6206 (ttp) REVERT: C 281 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.7723 (t) REVERT: C 313 TRP cc_start: 0.7787 (OUTLIER) cc_final: 0.7338 (t60) REVERT: C 325 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: C 403 MET cc_start: 0.3387 (mpp) cc_final: 0.3090 (mpp) REVERT: D 408 MET cc_start: -0.0625 (OUTLIER) cc_final: -0.0858 (mmp) REVERT: D 503 MET cc_start: 0.3269 (mtp) cc_final: 0.2685 (mtt) REVERT: D 700 TYR cc_start: 0.2773 (t80) cc_final: 0.1850 (t80) outliers start: 100 outliers final: 84 residues processed: 303 average time/residue: 0.4020 time to fit residues: 210.7940 Evaluate side-chains 307 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 211 time to evaluate : 3.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 313 TRP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 812 TYR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 0.9980 chunk 428 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 279 optimal weight: 4.9990 chunk 117 optimal weight: 30.0000 chunk 476 optimal weight: 0.0970 chunk 395 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 157 optimal weight: 0.0770 chunk 249 optimal weight: 0.8980 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS C 349 HIS ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35118 Z= 0.161 Angle : 0.551 12.975 47903 Z= 0.270 Chirality : 0.042 0.306 5724 Planarity : 0.003 0.075 6125 Dihedral : 8.087 82.319 5946 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.03 % Allowed : 19.48 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % 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: -1.36 (0.12), residues: 4922 helix: 0.78 (0.12), residues: 1864 sheet: -1.50 (0.17), residues: 852 loop : -2.17 (0.12), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 606 HIS 0.003 0.001 HIS B 435 PHE 0.024 0.001 PHE C 603 TYR 0.017 0.001 TYR B 280 ARG 0.005 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 217 time to evaluate : 3.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7594 (mm-40) REVERT: A 249 MET cc_start: 0.6453 (mmm) cc_final: 0.6114 (ttp) REVERT: A 252 TRP cc_start: 0.4778 (t60) cc_final: 0.4381 (t60) REVERT: A 281 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7423 (t) REVERT: A 313 TRP cc_start: 0.7628 (OUTLIER) cc_final: 0.7167 (t60) REVERT: A 325 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7715 (mp10) REVERT: A 403 MET cc_start: 0.3129 (mpp) cc_final: 0.2860 (mpp) REVERT: B 408 MET cc_start: -0.0317 (mmp) cc_final: -0.0655 (mmp) REVERT: B 700 TYR cc_start: 0.2528 (t80) cc_final: 0.2033 (t80) REVERT: C 106 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7607 (mm-40) REVERT: C 252 TRP cc_start: 0.4793 (t60) cc_final: 0.4423 (t60) REVERT: C 281 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7220 (t) REVERT: C 325 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: C 403 MET cc_start: 0.3344 (mpp) cc_final: 0.3067 (mpp) REVERT: C 666 MET cc_start: 0.7175 (mpp) cc_final: 0.6967 (mpp) REVERT: D 407 MET cc_start: 0.3272 (OUTLIER) cc_final: 0.2110 (pmm) REVERT: D 408 MET cc_start: -0.0414 (mmp) cc_final: -0.0784 (mmp) REVERT: D 700 TYR cc_start: 0.2568 (t80) cc_final: 0.1810 (t80) outliers start: 81 outliers final: 59 residues processed: 286 average time/residue: 0.4097 time to fit residues: 206.2332 Evaluate side-chains 269 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 202 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 812 TYR Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 271 optimal weight: 30.0000 chunk 347 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 400 optimal weight: 30.0000 chunk 265 optimal weight: 0.5980 chunk 474 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 18 GLN B 141 GLN B 435 HIS ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.168 35118 Z= 0.843 Angle : 0.933 14.153 47903 Z= 0.478 Chirality : 0.055 0.281 5724 Planarity : 0.006 0.139 6125 Dihedral : 9.802 94.783 5946 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.78 % Favored : 92.04 % Rotamer: Outliers : 4.95 % Allowed : 18.81 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % 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: -1.95 (0.12), residues: 4922 helix: 0.15 (0.12), residues: 1858 sheet: -1.62 (0.18), residues: 828 loop : -2.44 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 606 HIS 0.014 0.003 HIS A 21 PHE 0.027 0.003 PHE D 70 TYR 0.046 0.003 TYR A 71 ARG 0.014 0.001 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 212 time to evaluate : 4.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7930 (mm-40) REVERT: A 142 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7712 (tpm-80) REVERT: A 281 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8057 (p) REVERT: A 313 TRP cc_start: 0.7935 (OUTLIER) cc_final: 0.7475 (t60) REVERT: A 325 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7655 (mp10) REVERT: A 403 MET cc_start: 0.3227 (mpp) cc_final: 0.2987 (mpp) REVERT: A 581 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5673 (tmm) REVERT: B 29 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7542 (tp40) REVERT: B 106 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: B 408 MET cc_start: -0.0275 (mmp) cc_final: -0.0583 (mmp) REVERT: B 503 MET cc_start: 0.3205 (mtp) cc_final: 0.2626 (mtt) REVERT: B 700 TYR cc_start: 0.2988 (t80) cc_final: 0.2300 (t80) REVERT: C 106 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8048 (mm-40) REVERT: C 142 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7718 (tpm-80) REVERT: C 281 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8067 (p) REVERT: C 313 TRP cc_start: 0.7985 (OUTLIER) cc_final: 0.7557 (t60) REVERT: C 325 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7650 (mp10) REVERT: C 403 MET cc_start: 0.3508 (mpp) cc_final: 0.3250 (mpp) REVERT: C 666 MET cc_start: 0.7037 (mpp) cc_final: 0.6806 (mpp) REVERT: D 29 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7558 (tp40) REVERT: D 407 MET cc_start: 0.2867 (OUTLIER) cc_final: 0.1576 (pmm) REVERT: D 408 MET cc_start: -0.0448 (mmp) cc_final: -0.0775 (mmp) REVERT: D 700 TYR cc_start: 0.2852 (t80) cc_final: 0.2058 (t80) outliers start: 132 outliers final: 99 residues processed: 337 average time/residue: 0.3929 time to fit residues: 230.3487 Evaluate side-chains 320 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 206 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 313 TRP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 812 TYR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 605 TRP Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 91 CYS Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 0.4980 chunk 189 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 301 optimal weight: 30.0000 chunk 323 optimal weight: 50.0000 chunk 234 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 372 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35118 Z= 0.239 Angle : 0.619 13.208 47903 Z= 0.305 Chirality : 0.043 0.302 5724 Planarity : 0.003 0.056 6125 Dihedral : 8.706 82.914 5946 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.18 % Allowed : 20.94 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % 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: -1.50 (0.12), residues: 4922 helix: 0.61 (0.12), residues: 1858 sheet: -1.53 (0.18), residues: 840 loop : -2.20 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 606 HIS 0.003 0.001 HIS D 208 PHE 0.025 0.002 PHE C 603 TYR 0.020 0.001 TYR D 280 ARG 0.005 0.000 ARG C 624 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 209 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7779 (mm-40) REVERT: A 252 TRP cc_start: 0.4762 (t60) cc_final: 0.4335 (t60) REVERT: A 281 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.7714 (t) REVERT: A 313 TRP cc_start: 0.7686 (OUTLIER) cc_final: 0.7209 (t60) REVERT: A 325 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7610 (mp10) REVERT: A 403 MET cc_start: 0.3244 (mpp) cc_final: 0.3038 (mpp) REVERT: B 407 MET cc_start: 0.3340 (OUTLIER) cc_final: 0.1809 (pmm) REVERT: B 408 MET cc_start: -0.0287 (mmp) cc_final: -0.0602 (mmp) REVERT: B 700 TYR cc_start: 0.2744 (t80) cc_final: 0.2138 (t80) REVERT: C 106 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7771 (mm-40) REVERT: C 252 TRP cc_start: 0.4867 (t60) cc_final: 0.4397 (t60) REVERT: C 281 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7637 (t) REVERT: C 313 TRP cc_start: 0.7681 (OUTLIER) cc_final: 0.7223 (t60) REVERT: C 325 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: C 403 MET cc_start: 0.3446 (mpp) cc_final: 0.3226 (mpp) REVERT: D 407 MET cc_start: 0.2853 (OUTLIER) cc_final: 0.1519 (pmm) REVERT: D 408 MET cc_start: -0.0281 (mmp) cc_final: -0.0616 (mmp) REVERT: D 700 TYR cc_start: 0.2226 (t80) cc_final: 0.1742 (t80) REVERT: E 11 MET cc_start: 0.4599 (ppp) cc_final: 0.4237 (ptt) outliers start: 85 outliers final: 65 residues processed: 286 average time/residue: 0.4152 time to fit residues: 206.2028 Evaluate side-chains 274 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 199 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 313 TRP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 812 TYR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 6.9990 chunk 454 optimal weight: 6.9990 chunk 414 optimal weight: 9.9990 chunk 441 optimal weight: 0.2980 chunk 265 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 346 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 399 optimal weight: 50.0000 chunk 417 optimal weight: 3.9990 chunk 440 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 35118 Z= 0.347 Angle : 0.655 15.243 47903 Z= 0.324 Chirality : 0.044 0.282 5724 Planarity : 0.004 0.049 6125 Dihedral : 8.622 81.775 5946 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.33 % Allowed : 20.72 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % 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: -1.46 (0.12), residues: 4922 helix: 0.65 (0.12), residues: 1858 sheet: -1.50 (0.17), residues: 862 loop : -2.19 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 606 HIS 0.008 0.001 HIS C 349 PHE 0.025 0.002 PHE C 603 TYR 0.025 0.001 TYR A 71 ARG 0.004 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 202 time to evaluate : 4.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7859 (mm-40) REVERT: A 142 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7579 (tpm-80) REVERT: A 281 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.7706 (t) REVERT: A 313 TRP cc_start: 0.7663 (OUTLIER) cc_final: 0.7175 (t60) REVERT: A 325 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7650 (mp10) REVERT: A 666 MET cc_start: 0.7177 (mpp) cc_final: 0.6816 (mpp) REVERT: B 407 MET cc_start: 0.3379 (OUTLIER) cc_final: 0.1866 (pmm) REVERT: B 408 MET cc_start: -0.0191 (mmp) cc_final: -0.0499 (mmp) REVERT: B 700 TYR cc_start: 0.2805 (t80) cc_final: 0.2169 (t80) REVERT: C 106 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7824 (mm-40) REVERT: C 281 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7602 (t) REVERT: C 313 TRP cc_start: 0.7662 (OUTLIER) cc_final: 0.7189 (t60) REVERT: C 325 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: D 407 MET cc_start: 0.2775 (OUTLIER) cc_final: 0.1299 (pmm) REVERT: D 408 MET cc_start: -0.0030 (mmp) cc_final: -0.0358 (mmp) REVERT: D 503 MET cc_start: 0.4505 (mmm) cc_final: 0.3112 (tpp) outliers start: 89 outliers final: 75 residues processed: 284 average time/residue: 0.3982 time to fit residues: 197.7611 Evaluate side-chains 287 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 201 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 313 TRP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 812 TYR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 605 TRP Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 290 optimal weight: 9.9990 chunk 467 optimal weight: 40.0000 chunk 285 optimal weight: 30.0000 chunk 221 optimal weight: 0.9990 chunk 324 optimal weight: 6.9990 chunk 490 optimal weight: 20.0000 chunk 451 optimal weight: 30.0000 chunk 390 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 chunk 301 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 349 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN B 141 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 ASN D 18 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.126 35118 Z= 0.654 Angle : 0.836 13.948 47903 Z= 0.424 Chirality : 0.051 0.293 5724 Planarity : 0.005 0.109 6125 Dihedral : 9.518 86.339 5946 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.71 % Allowed : 20.38 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % 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: -1.81 (0.12), residues: 4922 helix: 0.27 (0.12), residues: 1854 sheet: -1.57 (0.17), residues: 850 loop : -2.36 (0.12), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP D 606 HIS 0.013 0.003 HIS C 209 PHE 0.028 0.003 PHE C 603 TYR 0.039 0.002 TYR C 71 ARG 0.013 0.001 ARG A 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 205 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.5485 (OUTLIER) cc_final: 0.4821 (pt) REVERT: A 106 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8000 (mm-40) REVERT: A 142 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7661 (tpm-80) REVERT: A 281 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8075 (t) REVERT: A 313 TRP cc_start: 0.7884 (OUTLIER) cc_final: 0.7428 (t60) REVERT: A 325 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: A 666 MET cc_start: 0.7292 (mpp) cc_final: 0.6972 (mpp) REVERT: B 29 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7257 (tp40) REVERT: B 408 MET cc_start: 0.0014 (mmp) cc_final: -0.0871 (mmp) REVERT: B 700 TYR cc_start: 0.2413 (t80) cc_final: 0.2059 (t80) REVERT: C 106 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8008 (mm-40) REVERT: C 142 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7681 (tpm-80) REVERT: C 281 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8119 (t) REVERT: C 313 TRP cc_start: 0.7884 (OUTLIER) cc_final: 0.7453 (t60) REVERT: C 325 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: C 666 MET cc_start: 0.6410 (mpp) cc_final: 0.6110 (mpp) REVERT: D 29 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7341 (tp40) REVERT: D 407 MET cc_start: 0.2566 (OUTLIER) cc_final: 0.0968 (pmm) REVERT: D 408 MET cc_start: -0.0178 (mmp) cc_final: -0.0512 (mmp) REVERT: D 503 MET cc_start: 0.4351 (mmm) cc_final: 0.3086 (tpp) outliers start: 99 outliers final: 80 residues processed: 298 average time/residue: 0.4208 time to fit residues: 218.9880 Evaluate side-chains 298 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 204 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 313 TRP Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 313 TRP Chi-restraints excluded: chain C residue 325 GLN Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 812 TYR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 203 TRP Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 203 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 9.9990 chunk 415 optimal weight: 30.0000 chunk 119 optimal weight: 9.9990 chunk 359 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 390 optimal weight: 20.0000 chunk 163 optimal weight: 0.5980 chunk 401 optimal weight: 50.0000 chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.201276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.171796 restraints weight = 71153.209| |-----------------------------------------------------------------------------| r_work (start): 0.4622 rms_B_bonded: 3.52 r_work: 0.4354 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work: 0.4302 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4262 r_free = 0.4262 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4262 r_free = 0.4262 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 35118 Z= 0.465 Angle : 0.713 13.306 47903 Z= 0.357 Chirality : 0.047 0.294 5724 Planarity : 0.004 0.052 6125 Dihedral : 9.097 82.439 5946 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.93 % Allowed : 20.23 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % 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: -1.67 (0.12), residues: 4922 helix: 0.44 (0.12), residues: 1856 sheet: -1.58 (0.17), residues: 848 loop : -2.29 (0.12), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 606 HIS 0.009 0.002 HIS C 349 PHE 0.028 0.002 PHE C 603 TYR 0.038 0.002 TYR A 529 ARG 0.005 0.001 ARG A 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7980.24 seconds wall clock time: 144 minutes 53.36 seconds (8693.36 seconds total)