Starting phenix.real_space_refine on Thu Feb 22 15:00:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lde_23284/02_2024/7lde_23284_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lde_23284/02_2024/7lde_23284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lde_23284/02_2024/7lde_23284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lde_23284/02_2024/7lde_23284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lde_23284/02_2024/7lde_23284_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lde_23284/02_2024/7lde_23284_neut_updated.pdb" } resolution = 3.9 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= 0.014 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 22102 2.51 5 N 5791 2.21 5 O 6359 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 120": "OD1" <-> "OD2" Residue "A ASP 134": "OD1" <-> "OD2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 219": "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 356": "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 TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "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 13": "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 173": "OD1" <-> "OD2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 295": "OD1" <-> "OD2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C ASP 367": "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 TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 110": "OD1" <-> "OD2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 223": "OD1" <-> "OD2" 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34424 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 5858 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 776, 5857 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 7, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 191 Conformer: "B" Number of residues, atoms: 776, 5857 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 7, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 191 bond proxies already assigned to first conformer: 5989 Chain: "B" Number of atoms: 5652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5652 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 415 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 267 Chain: "C" Number of atoms: 5858 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 776, 5857 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 7, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 191 Conformer: "B" Number of residues, atoms: 776, 5857 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 749} Chain breaks: 2 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 7, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 191 bond proxies already assigned to first conformer: 5989 Chain: "D" Number of atoms: 5652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5652 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 572 Unresolved non-hydrogen dihedrals: 415 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 267 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: "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: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 114 Unusual residues: {'D10': 1, 'HP6': 2, 'NAG': 3, 'OCT': 1, 'R16': 1, 'ZK1': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 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: 25.55, per 1000 atoms: 0.74 Number of scatterers: 34424 At special positions: 0 Unit cell: (133.914, 228.559, 276.889, 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 6359 8.00 N 5791 7.00 C 22102 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-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 C 908 " - " ASN C 345 " " 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 D 235 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.58 Conformation dependent library (CDL) restraints added in 11.0 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: 135 helices and 48 sheets defined 35.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.47 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 49 through 62 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 139 through 150 Processing helix chain 'A' and resid 164 through 176 Processing helix chain 'A' and resid 188 through 200 removed outlier: 3.868A pdb=" N GLN A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LYS A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 243 through 258 Processing helix chain 'A' and resid 270 through 291 Processing helix chain 'A' and resid 314 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: 5.295A 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: 3.662A 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 50 through 61 Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.545A pdb=" N LEU B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 4.184A 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 257 Processing helix chain 'B' and resid 274 through 295 Processing helix chain 'B' and resid 318 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: 4.349A 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: 5.881A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.770A 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 21 through 28 Processing helix chain 'C' and resid 49 through 62 Processing helix chain 'C' and resid 76 through 86 removed outlier: 3.729A pdb=" N THR C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 122 Processing helix chain 'C' and resid 138 through 149 removed outlier: 3.710A 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 200 removed outlier: 3.981A pdb=" N GLN C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LYS C 200 " --> pdb=" O GLY C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.692A pdb=" N ALA C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 291 Processing helix chain 'C' and resid 314 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: 3.932A pdb=" N LEU C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.510A 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: 4.040A 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: 5.244A 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: 3.536A 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 61 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 167 through 180 removed outlier: 3.573A pdb=" N ARG D 172 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 247 through 257 Processing helix chain 'D' and resid 274 through 295 Processing helix chain 'D' and resid 318 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: 3.653A 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: 6.167A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 5.807A 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: 3.811A 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: 3.999A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.566A 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: 3.501A 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: 3.505A 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: 3.584A pdb=" N GLY E 92 " --> pdb=" O TRP E 88 " (cutoff:3.500A) removed outlier: 4.563A 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: 3.604A 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: 3.901A 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: 3.662A 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: 3.573A 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: 3.980A 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: 3.631A pdb=" N PHE F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 removed outlier: 3.569A 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: 3.746A 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: 3.847A 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: 3.574A 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: 4.118A pdb=" N LEU G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) removed outlier: 4.092A 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: 4.312A 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: 3.709A 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: 3.554A 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: 3.642A 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: 4.119A pdb=" N LEU H 34 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 4.092A 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: 3.977A 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: 4.312A 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: 3.591A pdb=" N ALA H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 3.771A 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: 3.665A pdb=" N TYR H 179 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 3.665A 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: 4.091A pdb=" N GLY H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY H 209 " --> pdb=" O PHE H 205 " (cutoff:3.500A) removed outlier: 3.640A 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: 4.052A 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: 3.641A pdb=" N TYR H 226 " --> pdb=" O ALA H 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'K' and resid 161 through 164 Processing helix chain 'L' and resid 65 through 67 No H-bonds generated for 'chain 'L' and resid 65 through 67' Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' 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 184 through 189 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: 7.237A pdb=" N ALA A 66 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU A 12 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE A 68 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 153 through 158 removed outlier: 3.794A pdb=" N THR A 155 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 181 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 211 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 235 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 232 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY A 362 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU A 352 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS A 360 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 327 through 329 removed outlier: 3.671A pdb=" N PHE A 328 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 392 through 395 removed outlier: 6.458A pdb=" N ARG A 437 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 8.052A 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= E Processing sheet with id= F, 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: 8.547A 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= G, first strand: chain 'B' and resid 5 through 7 removed outlier: 6.817A pdb=" N ARG B 36 " --> pdb=" O ILE B 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.618A pdb=" N PHE B 12 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.728A pdb=" N SER B 89 " --> pdb=" O ILE B 67 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 153 through 158 removed outlier: 3.704A pdb=" N THR B 155 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 131 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ARG B 185 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS B 213 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU B 188 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE B 215 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 237 through 240 removed outlier: 3.948A pdb=" N GLY B 366 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU B 356 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS B 364 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.724A pdb=" N VAL B 332 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.709A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 7.083A 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: 7.737A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 36 through 43 removed outlier: 3.754A pdb=" N PHE C 13 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA C 66 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N LEU C 12 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE C 68 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 90 through 92 Processing sheet with id= P, first strand: chain 'C' and resid 153 through 158 removed outlier: 3.733A pdb=" N THR C 155 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU C 181 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 182 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 232 " --> pdb=" O MET C 353 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 362 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU C 352 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS C 360 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 392 through 395 removed outlier: 6.457A 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= Q Processing sheet with id= R, 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: 8.564A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 6.918A 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= S, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.569A pdb=" N PHE D 12 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 66 through 68 removed outlier: 6.661A pdb=" N SER D 89 " --> pdb=" O ILE D 67 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 153 through 158 removed outlier: 3.506A pdb=" N PHE D 127 " --> pdb=" O GLN D 153 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR D 155 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 131 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG D 185 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N HIS D 213 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU D 188 " --> pdb=" O HIS D 213 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE D 215 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 239 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL D 236 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY D 366 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU D 356 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS D 364 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing sheet with id= V, 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: 7.088A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.724A 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= W, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.626A pdb=" N LYS I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 139 through 141 Processing sheet with id= Y, first strand: chain 'I' and resid 144 through 147 removed outlier: 6.916A pdb=" N LYS I 241 " --> pdb=" O LEU I 145 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL I 147 " --> pdb=" O LYS I 241 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU I 243 " --> pdb=" O VAL I 147 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 12 through 14 Processing sheet with id= AA, first strand: chain 'J' and resid 21 through 25 removed outlier: 3.602A pdb=" N LEU J 74 " --> pdb=" O ILE J 22 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 88 through 91 Processing sheet with id= AC, first strand: chain 'J' and resid 130 through 134 Processing sheet with id= AD, first strand: chain 'J' and resid 154 through 156 removed outlier: 3.587A pdb=" N TRP J 149 " --> pdb=" O ARG J 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR J 193 " --> pdb=" O PHE J 210 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 4 through 8 removed outlier: 3.858A pdb=" N LYS K 6 " --> pdb=" O THR K 24 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 19 through 21 Processing sheet with id= AG, first strand: chain 'K' and resid 93 through 97 removed outlier: 3.530A pdb=" N MET K 93 " --> pdb=" O GLN K 40 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG K 39 " --> pdb=" O TRP K 48 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP K 48 " --> pdb=" O ARG K 39 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL K 51 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN K 59 " --> pdb=" O VAL K 51 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 147 through 149 Processing sheet with id= AI, first strand: chain 'K' and resid 202 through 205 Processing sheet with id= AJ, first strand: chain 'L' and resid 3 through 7 removed outlier: 3.944A pdb=" N SER L 21 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 139 through 141 Processing sheet with id= AL, first strand: chain 'L' and resid 144 through 147 removed outlier: 6.881A pdb=" N LYS L 241 " --> pdb=" O LEU L 145 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N VAL L 147 " --> pdb=" O LYS L 241 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLU L 243 " --> pdb=" O VAL L 147 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 21 through 24 Processing sheet with id= AN, first strand: chain 'M' and resid 86 through 89 Processing sheet with id= AO, first strand: chain 'M' and resid 154 through 156 removed outlier: 3.909A pdb=" N TRP M 149 " --> pdb=" O ARG M 156 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 160 through 162 removed outlier: 3.947A pdb=" N LEU M 161 " --> pdb=" O THR M 179 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR M 179 " --> pdb=" O LEU M 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'N' and resid 4 through 8 removed outlier: 3.593A pdb=" N SER N 26 " --> pdb=" O GLN N 4 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS N 6 " --> pdb=" O THR N 24 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'N' and resid 19 through 21 Processing sheet with id= AS, first strand: chain 'N' and resid 93 through 97 removed outlier: 5.977A pdb=" N ARG N 39 " --> pdb=" O TRP N 48 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TRP N 48 " --> pdb=" O ARG N 39 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'N' and resid 127 through 130 removed outlier: 3.690A pdb=" N SER N 127 " --> pdb=" O LYS N 150 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'N' and resid 142 through 144 Processing sheet with id= AV, first strand: chain 'N' and resid 158 through 161 removed outlier: 3.516A pdb=" N THR N 160 " --> pdb=" O ASN N 203 " (cutoff:3.500A) 1376 hydrogen bonds defined for protein. 3864 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: 13.43 Time building geometry restraints manager: 18.61 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: 11340 1.36 - 1.49: 8967 1.49 - 1.62: 14473 1.62 - 1.75: 0 1.75 - 1.88: 234 Bond restraints: 35014 Sorted by residual: bond pdb=" CAU ZK1 A 901 " pdb=" OAB ZK1 A 901 " ideal model delta sigma weight residual 1.215 1.404 -0.189 2.00e-02 2.50e+03 8.89e+01 bond pdb=" CAU ZK1 C 901 " pdb=" OAB ZK1 C 901 " ideal model delta sigma weight residual 1.215 1.404 -0.189 2.00e-02 2.50e+03 8.89e+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 D 906 " pdb=" OAB ZK1 D 906 " ideal model delta sigma weight residual 1.215 1.403 -0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" CAT ZK1 D 906 " pdb=" OAA ZK1 D 906 " ideal model delta sigma weight residual 1.214 1.395 -0.181 2.00e-02 2.50e+03 8.16e+01 ... (remaining 35009 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.99: 699 106.99 - 113.77: 19455 113.77 - 120.55: 13543 120.55 - 127.33: 13794 127.33 - 134.11: 263 Bond angle restraints: 47754 Sorted by residual: angle pdb=" CAM ZK1 D 906 " pdb=" NAX ZK1 D 906 " pdb=" CAN ZK1 D 906 " ideal model delta sigma weight residual 111.06 119.93 -8.87 3.00e+00 1.11e-01 8.74e+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 8.65e+00 angle pdb=" CAM ZK1 B 901 " pdb=" NAX ZK1 B 901 " pdb=" CAN ZK1 B 901 " ideal model delta sigma weight residual 111.06 119.86 -8.80 3.00e+00 1.11e-01 8.61e+00 angle pdb=" CAM ZK1 C 901 " pdb=" NAX ZK1 C 901 " pdb=" CAN ZK1 C 901 " ideal model delta sigma weight residual 111.06 119.84 -8.78 3.00e+00 1.11e-01 8.57e+00 angle pdb=" CAN ZK1 B 901 " pdb=" NAX ZK1 B 901 " pdb=" CAR ZK1 B 901 " ideal model delta sigma weight residual 112.98 120.16 -7.18 3.00e+00 1.11e-01 5.73e+00 ... (remaining 47749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 19898 23.74 - 47.48: 513 47.48 - 71.23: 48 71.23 - 94.97: 26 94.97 - 118.71: 21 Dihedral angle restraints: 20506 sinusoidal: 6172 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 93.00 131.75 -38.75 1 1.00e+01 1.00e-02 2.11e+01 ... (remaining 20503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.326: 5684 0.326 - 0.652: 2 0.652 - 0.978: 1 0.978 - 1.305: 0 1.305 - 1.631: 2 Chirality restraints: 5689 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-02 2.50e+03 6.65e+03 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 -1.08 -1.32 2.00e-02 2.50e+03 4.39e+03 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-02 2.50e+03 2.26e+03 ... (remaining 5686 not shown) Planarity restraints: 6126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 244 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.71e+00 pdb=" N PRO A 245 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 244 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO C 245 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 245 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 245 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 92 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 93 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.016 5.00e-02 4.00e+02 ... (remaining 6123 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 2 2.22 - 2.89: 13213 2.89 - 3.56: 46159 3.56 - 4.23: 72929 4.23 - 4.90: 121622 Nonbonded interactions: 253925 Sorted by model distance: nonbonded pdb=" NZ LYS C 178 " pdb=" O TYR C 465 " model vdw 1.548 2.520 nonbonded pdb=" NZ LYS C 178 " pdb=" C TYR C 465 " model vdw 2.188 3.350 nonbonded pdb=" OE2 GLU D 179 " pdb=" NZ LYS D 207 " model vdw 2.229 2.520 nonbonded pdb=" O4 NAG P 1 " pdb=" O7 NAG P 1 " model vdw 2.231 2.440 nonbonded pdb=" O4 NAG S 1 " pdb=" O7 NAG S 1 " model vdw 2.241 2.440 ... (remaining 253920 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 907)) selection = (chain 'C' and (resid 1 through 649 or resid 651 through 813 or resid 901 throug \ h 907)) } 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' } 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 group one per residue 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: 17.440 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: 0.000 Extract box with map and model: 35.010 Check model and map are aligned: 2.200 Set scattering table: 0.000 Process input model: 109.050 Find NCS groups from input model: 2.970 Set up NCS constraints: 0.500 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5557 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 0.189 35014 Z= 0.296 Angle : 0.473 8.871 47754 Z= 0.241 Chirality : 0.050 1.631 5689 Planarity : 0.002 0.033 6114 Dihedral : 11.880 118.710 11260 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: -3.63 (0.10), residues: 4922 helix: -1.50 (0.10), residues: 1850 sheet: -2.99 (0.16), residues: 849 loop : -2.92 (0.11), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.000 TRP A 252 HIS 0.001 0.000 HIS B 101 PHE 0.015 0.001 PHE A 24 TYR 0.008 0.000 TYR D 533 ARG 0.002 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 279 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 3.943 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 43 ILE cc_start: 0.8690 (mm) cc_final: 0.8480 (mm) REVERT: A 249 MET cc_start: 0.5436 (mmm) cc_final: 0.5062 (ttp) REVERT: C 249 MET cc_start: 0.4511 (mmm) cc_final: 0.3618 (ttp) REVERT: C 265 TRP cc_start: 0.1798 (m100) cc_final: 0.0646 (m100) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.4723 time to fit residues: 214.2231 Evaluate side-chains 148 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 4.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 206 optimal weight: 30.0000 chunk 127 optimal weight: 30.0000 chunk 251 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 chunk 385 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 234 optimal weight: 0.5980 chunk 287 optimal weight: 10.0000 chunk 446 optimal weight: 9.9990 overall best weight: 7.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN A 583 GLN A 722 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN B 764 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 571 ASN ** C 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN D 268 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN E 132 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.121 35014 Z= 0.706 Angle : 0.969 16.357 47754 Z= 0.509 Chirality : 0.053 0.298 5689 Planarity : 0.007 0.136 6114 Dihedral : 9.275 100.253 5921 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.52 % Favored : 93.25 % Rotamer: Outliers : 1.79 % Allowed : 11.73 % Favored : 86.48 % 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: -2.93 (0.11), residues: 4922 helix: -0.59 (0.11), residues: 1853 sheet: -2.89 (0.16), residues: 827 loop : -2.74 (0.11), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 313 HIS 0.020 0.003 HIS C 349 PHE 0.058 0.004 PHE C 337 TYR 0.047 0.003 TYR C 346 ARG 0.024 0.002 ARG A 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 209 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 162 time to evaluate : 4.146 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: C 346 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7982 (m-10) REVERT: C 363 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7198 (p90) REVERT: D 628 ARG cc_start: 0.5631 (OUTLIER) cc_final: 0.5199 (mtm180) REVERT: E 81 MET cc_start: 0.6993 (ptm) cc_final: 0.6715 (ptp) outliers start: 47 outliers final: 30 residues processed: 206 average time/residue: 0.4303 time to fit residues: 152.9964 Evaluate side-chains 172 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 3.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 768 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 371 optimal weight: 20.0000 chunk 304 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 447 optimal weight: 7.9990 chunk 483 optimal weight: 50.0000 chunk 398 optimal weight: 0.3980 chunk 443 optimal weight: 40.0000 chunk 152 optimal weight: 4.9990 chunk 359 optimal weight: 6.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 87 HIS C 101 ASN C 223 ASN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS C 355 HIS ** C 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** 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: 0.6093 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 35014 Z= 0.409 Angle : 0.659 14.125 47754 Z= 0.344 Chirality : 0.045 0.243 5689 Planarity : 0.004 0.069 6114 Dihedral : 8.568 99.866 5921 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.44 % Allowed : 13.90 % Favored : 83.66 % 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: -2.39 (0.11), residues: 4922 helix: 0.07 (0.12), residues: 1865 sheet: -2.81 (0.16), residues: 899 loop : -2.50 (0.12), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 522 HIS 0.009 0.002 HIS C 349 PHE 0.037 0.002 PHE A 26 TYR 0.026 0.002 TYR C 346 ARG 0.007 0.001 ARG A 293 *********************** 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 213 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 149 time to evaluate : 4.371 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: A 625 MET cc_start: 0.7826 (ppp) cc_final: 0.7308 (ppp) REVERT: C 363 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7162 (p90) REVERT: C 403 MET cc_start: 0.3764 (mpp) cc_final: 0.3293 (mpp) REVERT: E 81 MET cc_start: 0.7331 (ptm) cc_final: 0.6838 (mtm) outliers start: 64 outliers final: 37 residues processed: 202 average time/residue: 0.4348 time to fit residues: 154.6651 Evaluate side-chains 172 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 768 TYR Chi-restraints excluded: chain H residue 123 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 30.0000 chunk 336 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 213 optimal weight: 0.0470 chunk 300 optimal weight: 40.0000 chunk 449 optimal weight: 20.0000 chunk 475 optimal weight: 30.0000 chunk 234 optimal weight: 1.9990 chunk 425 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN C 722 ASN D 77 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 35014 Z= 0.161 Angle : 0.509 16.155 47754 Z= 0.259 Chirality : 0.042 0.293 5689 Planarity : 0.003 0.066 6114 Dihedral : 7.408 89.109 5921 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.22 % Allowed : 15.73 % Favored : 83.05 % 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: -1.73 (0.12), residues: 4922 helix: 0.72 (0.12), residues: 1846 sheet: -2.40 (0.17), residues: 839 loop : -2.28 (0.12), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 606 HIS 0.005 0.001 HIS D 268 PHE 0.039 0.002 PHE A 604 TYR 0.037 0.001 TYR B 797 ARG 0.007 0.000 ARG B 660 *********************** 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 172 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.3492 (OUTLIER) cc_final: 0.3263 (ptt) REVERT: A 625 MET cc_start: 0.7562 (ppp) cc_final: 0.7209 (ppp) REVERT: B 107 MET cc_start: 0.8303 (mmm) cc_final: 0.7953 (mtt) REVERT: C 403 MET cc_start: 0.3759 (OUTLIER) cc_final: 0.3313 (mpp) REVERT: D 670 MET cc_start: 0.7595 (ppp) cc_final: 0.7247 (ppp) REVERT: E 81 MET cc_start: 0.7297 (ptm) cc_final: 0.6806 (mtm) outliers start: 32 outliers final: 17 residues processed: 163 average time/residue: 0.4262 time to fit residues: 122.2656 Evaluate side-chains 149 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 4.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 768 TYR Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 40.0000 chunk 269 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 354 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 chunk 405 optimal weight: 40.0000 chunk 328 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 426 optimal weight: 40.0000 chunk 120 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 35014 Z= 0.431 Angle : 0.665 10.234 47754 Z= 0.348 Chirality : 0.045 0.293 5689 Planarity : 0.004 0.080 6114 Dihedral : 8.080 98.048 5921 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.89 % Favored : 93.09 % Rotamer: Outliers : 2.48 % Allowed : 15.62 % Favored : 81.90 % 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: -1.86 (0.12), residues: 4922 helix: 0.57 (0.12), residues: 1865 sheet: -2.55 (0.16), residues: 858 loop : -2.29 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 602 HIS 0.009 0.002 HIS B 40 PHE 0.032 0.002 PHE A 604 TYR 0.031 0.002 TYR C 346 ARG 0.017 0.001 ARG C 293 *********************** 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 207 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 142 time to evaluate : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 MET cc_start: 0.8597 (mmm) cc_final: 0.8337 (mtt) REVERT: C 346 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7840 (m-10) REVERT: C 363 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7177 (p90) REVERT: C 403 MET cc_start: 0.3747 (OUTLIER) cc_final: 0.3272 (mpp) REVERT: D 670 MET cc_start: 0.7624 (ppp) cc_final: 0.7295 (ppp) outliers start: 65 outliers final: 38 residues processed: 197 average time/residue: 0.4050 time to fit residues: 141.0604 Evaluate side-chains 177 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 136 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 768 TYR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain G residue 150 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 0.8980 chunk 428 optimal weight: 50.0000 chunk 94 optimal weight: 0.8980 chunk 279 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 476 optimal weight: 0.8980 chunk 395 optimal weight: 8.9990 chunk 220 optimal weight: 0.8980 chunk 39 optimal weight: 40.0000 chunk 157 optimal weight: 0.0270 chunk 249 optimal weight: 3.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 35014 Z= 0.146 Angle : 0.513 17.625 47754 Z= 0.261 Chirality : 0.042 0.321 5689 Planarity : 0.003 0.071 6114 Dihedral : 7.107 87.811 5921 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.07 % Allowed : 16.99 % Favored : 81.94 % 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: -1.35 (0.12), residues: 4922 helix: 1.08 (0.12), residues: 1851 sheet: -2.25 (0.17), residues: 845 loop : -2.08 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 606 HIS 0.004 0.001 HIS D 268 PHE 0.022 0.001 PHE A 527 TYR 0.033 0.001 TYR B 523 ARG 0.006 0.000 ARG B 24 *********************** 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 171 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 3.963 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: A 52 MET cc_start: 0.8912 (tpp) cc_final: 0.8614 (ttp) REVERT: C 403 MET cc_start: 0.3411 (OUTLIER) cc_final: 0.2937 (mpp) REVERT: D 355 MET cc_start: 0.8733 (mmm) cc_final: 0.8188 (mmt) REVERT: D 670 MET cc_start: 0.7624 (ppp) cc_final: 0.7402 (ppp) REVERT: E 11 MET cc_start: 0.7285 (mtt) cc_final: 0.7050 (mtm) outliers start: 28 outliers final: 18 residues processed: 164 average time/residue: 0.4135 time to fit residues: 120.3646 Evaluate side-chains 156 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 4.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 768 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 271 optimal weight: 40.0000 chunk 347 optimal weight: 30.0000 chunk 269 optimal weight: 6.9990 chunk 400 optimal weight: 30.0000 chunk 265 optimal weight: 6.9990 chunk 474 optimal weight: 9.9990 chunk 296 optimal weight: 40.0000 chunk 289 optimal weight: 10.0000 chunk 218 optimal weight: 30.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN ** C 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.103 35014 Z= 0.704 Angle : 0.893 15.645 47754 Z= 0.472 Chirality : 0.050 0.349 5689 Planarity : 0.006 0.124 6114 Dihedral : 9.032 108.691 5921 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.06 % Favored : 90.67 % Rotamer: Outliers : 2.90 % Allowed : 16.46 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.12), residues: 4922 helix: 0.31 (0.12), residues: 1852 sheet: -2.67 (0.16), residues: 869 loop : -2.31 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP B 606 HIS 0.015 0.003 HIS B 40 PHE 0.043 0.003 PHE A 26 TYR 0.049 0.003 TYR C 346 ARG 0.015 0.001 ARG A 25 *********************** 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 219 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 143 time to evaluate : 4.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8351 (tmm) cc_final: 0.7566 (tmm) REVERT: B 24 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7127 (mmt180) REVERT: B 91 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8982 (mm) REVERT: B 107 MET cc_start: 0.8503 (mmm) cc_final: 0.8226 (mtt) REVERT: B 355 MET cc_start: 0.7634 (mtt) cc_final: 0.7411 (mtt) REVERT: B 647 TYR cc_start: 0.6108 (OUTLIER) cc_final: 0.5280 (p90) REVERT: C 346 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7959 (m-10) REVERT: C 363 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7683 (p90) REVERT: D 670 MET cc_start: 0.7739 (ppp) cc_final: 0.7477 (ppp) REVERT: G 29 PHE cc_start: -0.1983 (OUTLIER) cc_final: -0.3529 (m-80) outliers start: 76 outliers final: 56 residues processed: 208 average time/residue: 0.4181 time to fit residues: 152.8815 Evaluate side-chains 196 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 134 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 768 TYR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain H residue 123 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 283 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 301 optimal weight: 7.9990 chunk 323 optimal weight: 20.0000 chunk 234 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 372 optimal weight: 40.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35014 Z= 0.198 Angle : 0.569 16.092 47754 Z= 0.292 Chirality : 0.043 0.346 5689 Planarity : 0.003 0.074 6114 Dihedral : 7.737 93.721 5921 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.22 % Allowed : 18.55 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.12), residues: 4922 helix: 0.93 (0.12), residues: 1849 sheet: -2.38 (0.16), residues: 876 loop : -2.07 (0.13), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.002 TRP B 606 HIS 0.005 0.001 HIS D 268 PHE 0.024 0.002 PHE A 603 TYR 0.019 0.001 TYR C 71 ARG 0.010 0.001 ARG A 293 *********************** 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 171 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 3.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8985 (tpp) cc_final: 0.8770 (ttp) REVERT: B 107 MET cc_start: 0.8541 (mmm) cc_final: 0.8312 (mtt) REVERT: C 52 MET cc_start: 0.8248 (tpp) cc_final: 0.7652 (mtt) REVERT: C 403 MET cc_start: 0.3342 (OUTLIER) cc_final: 0.2959 (mpp) REVERT: F 11 MET cc_start: 0.5457 (mtt) cc_final: 0.4349 (tpp) REVERT: G 29 PHE cc_start: -0.2053 (OUTLIER) cc_final: -0.3640 (m-80) outliers start: 32 outliers final: 23 residues processed: 165 average time/residue: 0.4101 time to fit residues: 121.0749 Evaluate side-chains 161 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain G residue 29 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 20.0000 chunk 454 optimal weight: 4.9990 chunk 414 optimal weight: 9.9990 chunk 441 optimal weight: 50.0000 chunk 265 optimal weight: 0.0570 chunk 192 optimal weight: 10.0000 chunk 346 optimal weight: 30.0000 chunk 135 optimal weight: 6.9990 chunk 399 optimal weight: 50.0000 chunk 417 optimal weight: 9.9990 chunk 440 optimal weight: 50.0000 overall best weight: 6.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 ASN ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 35014 Z= 0.551 Angle : 0.797 17.636 47754 Z= 0.418 Chirality : 0.048 0.318 5689 Planarity : 0.005 0.087 6114 Dihedral : 8.950 105.170 5921 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.39 % Favored : 90.49 % Rotamer: Outliers : 2.02 % Allowed : 17.94 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.12), residues: 4922 helix: 0.41 (0.12), residues: 1863 sheet: -2.61 (0.16), residues: 848 loop : -2.23 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP B 606 HIS 0.014 0.002 HIS D 40 PHE 0.035 0.003 PHE A 26 TYR 0.037 0.002 TYR C 346 ARG 0.010 0.001 ARG A 25 *********************** 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 192 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 139 time to evaluate : 4.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8296 (tmm) cc_final: 0.7516 (tmm) REVERT: B 91 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8946 (mm) REVERT: B 647 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.5213 (p90) REVERT: C 15 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8325 (p0) REVERT: C 403 MET cc_start: 0.3713 (OUTLIER) cc_final: 0.3298 (mpp) REVERT: D 585 MET cc_start: 0.5797 (tpp) cc_final: 0.5588 (tpp) REVERT: D 670 MET cc_start: 0.7540 (ppp) cc_final: 0.7199 (ppp) REVERT: G 29 PHE cc_start: -0.1853 (OUTLIER) cc_final: -0.3561 (m-80) outliers start: 53 outliers final: 38 residues processed: 182 average time/residue: 0.4096 time to fit residues: 132.3398 Evaluate side-chains 179 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 136 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain G residue 29 PHE 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: 50.0000 chunk 285 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 324 optimal weight: 50.0000 chunk 490 optimal weight: 8.9990 chunk 451 optimal weight: 0.7980 chunk 390 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 301 optimal weight: 2.9990 chunk 239 optimal weight: 0.5980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.201 35014 Z= 0.502 Angle : 0.871 59.200 47754 Z= 0.474 Chirality : 0.047 0.425 5689 Planarity : 0.005 0.086 6114 Dihedral : 8.946 105.070 5921 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.41 % Favored : 90.57 % Rotamer: Outliers : 1.87 % Allowed : 18.25 % Favored : 79.89 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.12), residues: 4922 helix: 0.39 (0.12), residues: 1862 sheet: -2.62 (0.16), residues: 850 loop : -2.24 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP B 606 HIS 0.013 0.002 HIS D 40 PHE 0.068 0.003 PHE B 584 TYR 0.035 0.002 TYR C 346 ARG 0.009 0.001 ARG C 624 ********************** 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 183 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 134 time to evaluate : 4.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8268 (tmm) cc_final: 0.7496 (tmm) REVERT: B 107 MET cc_start: 0.8407 (mtt) cc_final: 0.8127 (mtt) REVERT: B 647 TYR cc_start: 0.6029 (OUTLIER) cc_final: 0.5204 (p90) REVERT: C 403 MET cc_start: 0.3731 (OUTLIER) cc_final: 0.3294 (mpp) REVERT: D 585 MET cc_start: 0.5706 (tpp) cc_final: 0.5502 (tpp) REVERT: D 670 MET cc_start: 0.7510 (ppp) cc_final: 0.7195 (ppp) REVERT: G 29 PHE cc_start: -0.1848 (OUTLIER) cc_final: -0.3564 (m-80) outliers start: 49 outliers final: 41 residues processed: 171 average time/residue: 0.4056 time to fit residues: 125.1358 Evaluate side-chains 178 residues out of total 4276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 134 time to evaluate : 4.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 252 TRP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 602 TRP Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 252 TRP Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 714 CYS Chi-restraints excluded: chain C residue 787 ASN Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain G residue 29 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 10.0000 chunk 415 optimal weight: 40.0000 chunk 119 optimal weight: 40.0000 chunk 359 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 108 optimal weight: 0.0270 chunk 390 optimal weight: 20.0000 chunk 163 optimal weight: 0.5980 chunk 401 optimal weight: 40.0000 chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 3.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.085688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.063727 restraints weight = 228105.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.060531 restraints weight = 147779.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.060666 restraints weight = 121323.691| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.201 35014 Z= 0.502 Angle : 0.871 59.200 47754 Z= 0.474 Chirality : 0.047 0.425 5689 Planarity : 0.005 0.086 6114 Dihedral : 8.946 105.070 5921 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.41 % Favored : 90.57 % Rotamer: Outliers : 1.68 % Allowed : 18.44 % Favored : 79.89 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 15.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.12), residues: 4922 helix: 0.39 (0.12), residues: 1862 sheet: -2.62 (0.16), residues: 850 loop : -2.24 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP B 606 HIS 0.013 0.002 HIS D 40 PHE 0.068 0.003 PHE B 584 TYR 0.035 0.002 TYR C 346 ARG 0.009 0.001 ARG C 624 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6195.13 seconds wall clock time: 115 minutes 17.57 seconds (6917.57 seconds total)