Starting phenix.real_space_refine on Wed Jul 30 23:39:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mzj_9303/07_2025/6mzj_9303.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mzj_9303/07_2025/6mzj_9303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mzj_9303/07_2025/6mzj_9303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mzj_9303/07_2025/6mzj_9303.map" model { file = "/net/cci-nas-00/data/ceres_data/6mzj_9303/07_2025/6mzj_9303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mzj_9303/07_2025/6mzj_9303.cif" } resolution = 4.8 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= -0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 85 5.16 5 C 7441 2.51 5 N 2238 2.21 5 O 2889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12653 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 2842 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 423} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Unresolved non-hydrogen bonds: 1564 Unresolved non-hydrogen angles: 2026 Unresolved non-hydrogen dihedrals: 1299 Unresolved non-hydrogen chiralities: 167 Planarities with less than four sites: {'GLN:plan1': 25, 'ARG:plan': 24, 'TYR:plan': 16, 'ASN:plan1': 30, 'TRP:plan': 15, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 27, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 856 Chain: "L" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 506 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 170 Chain: "H" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 594 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 5, 'PCA:plan-2': 1, 'ASN:plan1': 5, 'TRP:plan': 5, 'HIS:plan': 2, 'TYR:plan': 8, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 234 Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 2842 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 423} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Unresolved non-hydrogen bonds: 1564 Unresolved non-hydrogen angles: 2026 Unresolved non-hydrogen dihedrals: 1299 Unresolved non-hydrogen chiralities: 167 Planarities with less than four sites: {'GLN:plan1': 25, 'ARG:plan': 24, 'TYR:plan': 16, 'ASN:plan1': 30, 'TRP:plan': 15, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 27, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 856 Chain: "C" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 506 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 170 Chain: "D" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 594 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 5, 'PCA:plan-2': 1, 'ASN:plan1': 5, 'TRP:plan': 5, 'HIS:plan': 2, 'TYR:plan': 8, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 234 Chain: "E" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 2842 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 423} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Unresolved non-hydrogen bonds: 1564 Unresolved non-hydrogen angles: 2026 Unresolved non-hydrogen dihedrals: 1299 Unresolved non-hydrogen chiralities: 167 Planarities with less than four sites: {'GLN:plan1': 25, 'ARG:plan': 24, 'TYR:plan': 16, 'ASN:plan1': 30, 'TRP:plan': 15, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 27, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 856 Chain: "F" 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: "G" 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "N" 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "b" 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" 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: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" 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: "h" 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: "i" 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: "j" 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: "k" 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: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" 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: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.44, per 1000 atoms: 0.75 Number of scatterers: 12653 At special positions: 0 Unit cell: (130.56, 141.44, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 85 16.00 O 2889 8.00 N 2238 7.00 C 7441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.13 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.05 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS H 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.20 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.17 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.13 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.05 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 459 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.20 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.17 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.14 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.05 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS E 605 " distance=2.20 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN R 4 " - " MAN R 5 " " MAN a 4 " - " MAN a 5 " " MAN f 4 " - " MAN f 5 " " MAN o 4 " - " MAN o 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 6 " " MAN J 4 " - " MAN J 5 " " BMA M 3 " - " MAN M 4 " " MAN M 6 " - " MAN M 7 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 6 " " MAN Y 4 " - " MAN Y 5 " " BMA a 3 " - " MAN a 4 " " MAN a 6 " - " MAN a 7 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA l 3 " - " MAN l 4 " " BMA o 3 " - " MAN o 4 " " MAN o 6 " - " MAN o 7 " " BMA r 3 " - " MAN r 4 " " BMA t 3 " - " MAN t 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " BMA M 3 " - " MAN M 6 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 6 " " BMA l 3 " - " MAN l 5 " " BMA o 3 " - " MAN o 6 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " NAG-ASN " NAG A 737 " - " ASN A 357 " " NAG A 743 " - " ASN A 411 " " NAG A 746 " - " ASN A 611 " " NAG A 747 " - " ASN A 637 " " NAG B 737 " - " ASN B 357 " " NAG B 743 " - " ASN B 411 " " NAG B 746 " - " ASN B 611 " " NAG B 747 " - " ASN B 637 " " NAG E 734 " - " ASN E 357 " " NAG E 739 " - " ASN E 411 " " NAG E 742 " - " ASN E 611 " " NAG E 743 " - " ASN E 637 " " NAG F 1 " - " ASN A 88 " " NAG G 1 " - " ASN A 130 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 241 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 289 " " NAG O 1 " - " ASN A 301 " " NAG P 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 337 " " NAG R 1 " - " ASN A 386 " " NAG S 1 " - " ASN A 442 " " NAG T 1 " - " ASN A 230 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN B 88 " " NAG W 1 " - " ASN B 130 " " NAG X 1 " - " ASN B 156 " " NAG Y 1 " - " ASN B 197 " " NAG Z 1 " - " ASN B 241 " " NAG a 1 " - " ASN B 262 " " NAG b 1 " - " ASN B 289 " " NAG c 1 " - " ASN B 301 " " NAG d 1 " - " ASN B 332 " " NAG e 1 " - " ASN B 337 " " NAG f 1 " - " ASN B 386 " " NAG g 1 " - " ASN B 442 " " NAG h 1 " - " ASN B 230 " " NAG i 1 " - " ASN B 392 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 130 " " NAG l 1 " - " ASN E 156 " " NAG m 1 " - " ASN E 197 " " NAG n 1 " - " ASN E 241 " " NAG o 1 " - " ASN E 262 " " NAG p 1 " - " ASN E 289 " " NAG q 1 " - " ASN E 301 " " NAG r 1 " - " ASN E 332 " " NAG s 1 " - " ASN E 337 " " NAG t 1 " - " ASN E 386 " " NAG u 1 " - " ASN E 442 " " NAG v 1 " - " ASN E 230 " " NAG w 1 " - " ASN E 392 " Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 1.8 seconds 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 39 sheets defined 23.2% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.230A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.769A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 Processing helix chain 'A' and resid 571 through 596 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.612A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 662 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 98 through 116 removed outlier: 4.228A pdb=" N ASP B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 334 through 353 removed outlier: 3.769A pdb=" N HIS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 571 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.612A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 removed outlier: 4.115A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.229A pdb=" N ASP E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.769A pdb=" N HIS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 481 Processing helix chain 'E' and resid 482 through 484 No H-bonds generated for 'chain 'E' and resid 482 through 484' Processing helix chain 'E' and resid 523 through 528 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 571 through 596 Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.613A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.266A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N CYS A 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.832A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.241A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.503A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY A 451 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N LYS A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.956A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N LEU A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N VAL A 286 " --> pdb=" O LEU A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 357 through 361 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.905A pdb=" N VAL A 286 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N LEU A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.956A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N LYS A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY A 451 " --> pdb=" O LYS A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 414 through 420 removed outlier: 3.576A pdb=" N PHE A 383 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.390A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.777A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.459A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.459A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.566A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AB7, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.266A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.832A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.240A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.502A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY B 451 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 10.780A pdb=" N LYS B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 10.906A pdb=" N VAL B 286 " --> pdb=" O LEU B 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 298 current: chain 'B' and resid 357 through 361 Processing sheet with id=AC5, first strand: chain 'B' and resid 271 through 273 removed outlier: 10.906A pdb=" N VAL B 286 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU B 288 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU B 453 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.780A pdb=" N LYS B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY B 451 " --> pdb=" O LYS B 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 443 through 456 current: chain 'B' and resid 414 through 420 removed outlier: 3.576A pdb=" N PHE B 383 " --> pdb=" O PHE B 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 302 through 312 removed outlier: 6.390A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.777A pdb=" N SER C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.459A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.459A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.566A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AD4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.266A pdb=" N VAL E 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL E 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR E 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR E 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N CYS E 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.832A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.240A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.502A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY E 451 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 10.780A pdb=" N LYS E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N VAL E 286 " --> pdb=" O LEU E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 357 through 361 Processing sheet with id=AE2, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.905A pdb=" N VAL E 286 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N LEU E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.962A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.780A pdb=" N LYS E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY E 451 " --> pdb=" O LYS E 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 414 through 420 removed outlier: 3.576A pdb=" N PHE E 383 " --> pdb=" O PHE E 376 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 302 through 312 removed outlier: 6.389A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1776 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: 5.44 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4338 1.33 - 1.45: 2132 1.45 - 1.58: 6140 1.58 - 1.70: 25 1.70 - 1.82: 85 Bond restraints: 12720 Sorted by residual: bond pdb=" C5 BMA M 3 " pdb=" C6 BMA M 3 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C5 BMA a 3 " pdb=" C6 BMA a 3 " ideal model delta sigma weight residual 1.526 1.610 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C5 BMA o 3 " pdb=" C6 BMA o 3 " ideal model delta sigma weight residual 1.526 1.609 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C5 BMA m 3 " pdb=" C6 BMA m 3 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C5 BMA J 3 " pdb=" C6 BMA J 3 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 12715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 14543 1.72 - 3.44: 2329 3.44 - 5.16: 399 5.16 - 6.87: 278 6.87 - 8.59: 86 Bond angle restraints: 17635 Sorted by residual: angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 126.39 -6.73 7.20e-01 1.93e+00 8.75e+01 angle pdb=" C ALA E 436 " pdb=" N PRO E 437 " pdb=" CA PRO E 437 " ideal model delta sigma weight residual 119.66 126.39 -6.73 7.20e-01 1.93e+00 8.73e+01 angle pdb=" C ALA B 436 " pdb=" N PRO B 437 " pdb=" CA PRO B 437 " ideal model delta sigma weight residual 119.66 126.38 -6.72 7.20e-01 1.93e+00 8.70e+01 angle pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 119.56 128.15 -8.59 1.01e+00 9.80e-01 7.24e+01 angle pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 119.56 128.13 -8.57 1.01e+00 9.80e-01 7.20e+01 ... (remaining 17630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 8957 21.75 - 43.49: 329 43.49 - 65.23: 83 65.23 - 86.98: 114 86.98 - 108.72: 84 Dihedral angle restraints: 9567 sinusoidal: 3607 harmonic: 5960 Sorted by residual: dihedral pdb=" CA PHE E 353 " pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta harmonic sigma weight residual 180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA PHE B 353 " pdb=" C PHE B 353 " pdb=" N PRO B 354 " pdb=" CA PRO B 354 " ideal model delta harmonic sigma weight residual 180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE A 353 " pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 9564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2442 0.131 - 0.261: 209 0.261 - 0.392: 20 0.392 - 0.522: 0 0.522 - 0.653: 21 Chirality restraints: 2692 Sorted by residual: chirality pdb=" C1 BMA o 3 " pdb=" O4 NAG o 2 " pdb=" C2 BMA o 3 " pdb=" O5 BMA o 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.92e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.92e+02 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.90e+02 ... (remaining 2689 not shown) Planarity restraints: 2359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 301 " -0.026 2.00e-02 2.50e+03 2.81e-02 9.84e+00 pdb=" CG ASN B 301 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN B 301 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 301 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG c 1 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 301 " -0.026 2.00e-02 2.50e+03 2.78e-02 9.67e+00 pdb=" CG ASN A 301 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 301 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 301 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 301 " -0.025 2.00e-02 2.50e+03 2.77e-02 9.61e+00 pdb=" CG ASN E 301 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN E 301 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN E 301 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG q 1 " -0.034 2.00e-02 2.50e+03 ... (remaining 2356 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 5364 2.86 - 3.37: 10411 3.37 - 3.88: 17431 3.88 - 4.39: 16909 4.39 - 4.90: 27905 Nonbonded interactions: 78020 Sorted by model distance: nonbonded pdb=" O3 NAG X 1 " pdb=" O5 NAG X 2 " model vdw 2.352 3.040 nonbonded pdb=" O3 NAG I 1 " pdb=" O5 NAG I 2 " model vdw 2.353 3.040 nonbonded pdb=" O3 NAG l 1 " pdb=" O5 NAG l 2 " model vdw 2.354 3.040 nonbonded pdb=" O3 NAG N 2 " pdb=" O7 NAG N 2 " model vdw 2.383 3.040 nonbonded pdb=" O3 NAG p 2 " pdb=" O7 NAG p 2 " model vdw 2.383 3.040 ... (remaining 78015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'b' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'p' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain 'I' selection = chain 'R' selection = chain 'X' selection = chain 'f' selection = chain 'l' } ncs_group { reference = (chain 'J' and (resid 1 or resid 4 through 6)) selection = (chain 'M' and (resid 2 or resid 5 through 7)) selection = (chain 'Y' and (resid 1 or resid 4 through 6)) selection = (chain 'a' and (resid 2 or resid 5 through 7)) selection = (chain 'o' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'Z' selection = chain 'c' selection = chain 'm' selection = chain 'n' selection = chain 'q' } ncs_group { reference = chain 'P' selection = chain 'd' selection = chain 'r' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 2.090 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: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.710 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 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:5.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 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 : 0.016 0.166 12911 Z= 0.852 Angle : 1.625 13.383 18166 Z= 0.929 Chirality : 0.093 0.653 2692 Planarity : 0.004 0.013 2305 Dihedral : 20.353 108.723 5547 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.23 % Favored : 96.62 % Rotamer: Outliers : 2.65 % Allowed : 5.31 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2042 helix: -0.09 (0.25), residues: 405 sheet: 0.10 (0.20), residues: 620 loop : -0.13 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.02284 ( 54) link_NAG-ASN : angle 2.40898 ( 162) link_ALPHA1-6 : bond 0.03283 ( 8) link_ALPHA1-6 : angle 2.42116 ( 24) link_BETA1-4 : bond 0.03087 ( 63) link_BETA1-4 : angle 1.78551 ( 189) link_ALPHA1-2 : bond 0.02838 ( 5) link_ALPHA1-2 : angle 1.01572 ( 15) link_ALPHA1-3 : bond 0.03309 ( 19) link_ALPHA1-3 : angle 1.27472 ( 57) hydrogen bonds : bond 0.19128 ( 634) hydrogen bonds : angle 7.92778 ( 1776) SS BOND : bond 0.06112 ( 42) SS BOND : angle 3.99642 ( 84) covalent geometry : bond 0.01496 (12720) covalent geometry : angle 1.59431 (17635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 1.279 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 45 average time/residue: 0.1188 time to fit residues: 11.6253 Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 30.0000 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.040774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.034229 restraints weight = 221729.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.034665 restraints weight = 174358.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.035024 restraints weight = 142934.570| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 12911 Z= 0.297 Angle : 1.124 22.643 18166 Z= 0.488 Chirality : 0.057 0.408 2692 Planarity : 0.005 0.035 2305 Dihedral : 12.460 84.197 5093 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 2042 helix: 1.21 (0.25), residues: 396 sheet: -0.05 (0.19), residues: 649 loop : -0.20 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.01015 ( 54) link_NAG-ASN : angle 4.32251 ( 162) link_ALPHA1-6 : bond 0.00758 ( 8) link_ALPHA1-6 : angle 2.61440 ( 24) link_BETA1-4 : bond 0.00632 ( 63) link_BETA1-4 : angle 2.84342 ( 189) link_ALPHA1-2 : bond 0.00146 ( 5) link_ALPHA1-2 : angle 2.11776 ( 15) link_ALPHA1-3 : bond 0.00774 ( 19) link_ALPHA1-3 : angle 3.71015 ( 57) hydrogen bonds : bond 0.05439 ( 634) hydrogen bonds : angle 6.05395 ( 1776) SS BOND : bond 0.00445 ( 42) SS BOND : angle 1.38478 ( 84) covalent geometry : bond 0.00507 (12720) covalent geometry : angle 0.98809 (17635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.350 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1124 time to fit residues: 9.2927 Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 86 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 184 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.038871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.032507 restraints weight = 224374.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.032937 restraints weight = 172743.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.033291 restraints weight = 140184.125| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 12911 Z= 0.273 Angle : 0.975 19.198 18166 Z= 0.422 Chirality : 0.055 0.598 2692 Planarity : 0.005 0.043 2305 Dihedral : 10.606 61.905 5093 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 2042 helix: 1.63 (0.26), residues: 420 sheet: -0.12 (0.20), residues: 648 loop : -0.53 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.01599 ( 54) link_NAG-ASN : angle 4.25625 ( 162) link_ALPHA1-6 : bond 0.01296 ( 8) link_ALPHA1-6 : angle 3.60546 ( 24) link_BETA1-4 : bond 0.00516 ( 63) link_BETA1-4 : angle 2.28411 ( 189) link_ALPHA1-2 : bond 0.00473 ( 5) link_ALPHA1-2 : angle 1.96789 ( 15) link_ALPHA1-3 : bond 0.00969 ( 19) link_ALPHA1-3 : angle 1.70903 ( 57) hydrogen bonds : bond 0.05066 ( 634) hydrogen bonds : angle 5.77484 ( 1776) SS BOND : bond 0.00410 ( 42) SS BOND : angle 1.25050 ( 84) covalent geometry : bond 0.00480 (12720) covalent geometry : angle 0.84794 (17635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1108 time to fit residues: 9.0394 Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 40.0000 chunk 206 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.037423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.031372 restraints weight = 230806.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.031751 restraints weight = 182216.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.032058 restraints weight = 150126.084| |-----------------------------------------------------------------------------| r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 12911 Z= 0.338 Angle : 1.145 19.820 18166 Z= 0.503 Chirality : 0.057 0.490 2692 Planarity : 0.006 0.046 2305 Dihedral : 10.630 59.167 5093 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.90 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.33 (0.18), residues: 2042 helix: 0.24 (0.25), residues: 429 sheet: -0.77 (0.20), residues: 643 loop : -1.41 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.01215 ( 54) link_NAG-ASN : angle 4.30080 ( 162) link_ALPHA1-6 : bond 0.01320 ( 8) link_ALPHA1-6 : angle 3.23088 ( 24) link_BETA1-4 : bond 0.00879 ( 63) link_BETA1-4 : angle 2.80048 ( 189) link_ALPHA1-2 : bond 0.00552 ( 5) link_ALPHA1-2 : angle 2.85517 ( 15) link_ALPHA1-3 : bond 0.00912 ( 19) link_ALPHA1-3 : angle 2.65388 ( 57) hydrogen bonds : bond 0.05368 ( 634) hydrogen bonds : angle 6.87735 ( 1776) SS BOND : bond 0.00555 ( 42) SS BOND : angle 1.37971 ( 84) covalent geometry : bond 0.00585 (12720) covalent geometry : angle 1.02149 (17635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.310 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1277 time to fit residues: 10.3264 Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 94 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 60 optimal weight: 0.0570 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 overall best weight: 3.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.037969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.031790 restraints weight = 230173.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.032180 restraints weight = 180852.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.032503 restraints weight = 148673.169| |-----------------------------------------------------------------------------| r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12911 Z= 0.190 Angle : 0.869 19.390 18166 Z= 0.370 Chirality : 0.051 0.420 2692 Planarity : 0.004 0.046 2305 Dihedral : 9.358 59.876 5093 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.19), residues: 2042 helix: 1.51 (0.26), residues: 411 sheet: -0.80 (0.20), residues: 646 loop : -1.28 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00870 ( 54) link_NAG-ASN : angle 3.76146 ( 162) link_ALPHA1-6 : bond 0.01043 ( 8) link_ALPHA1-6 : angle 3.28168 ( 24) link_BETA1-4 : bond 0.00443 ( 63) link_BETA1-4 : angle 2.15691 ( 189) link_ALPHA1-2 : bond 0.00498 ( 5) link_ALPHA1-2 : angle 2.43372 ( 15) link_ALPHA1-3 : bond 0.00909 ( 19) link_ALPHA1-3 : angle 1.65340 ( 57) hydrogen bonds : bond 0.03816 ( 634) hydrogen bonds : angle 5.85181 ( 1776) SS BOND : bond 0.00272 ( 42) SS BOND : angle 0.82495 ( 84) covalent geometry : bond 0.00335 (12720) covalent geometry : angle 0.75203 (17635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.366 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1142 time to fit residues: 9.4670 Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 22 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 198 optimal weight: 1.9990 chunk 61 optimal weight: 40.0000 chunk 175 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 203 optimal weight: 30.0000 chunk 148 optimal weight: 9.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.036503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.030291 restraints weight = 225740.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.030705 restraints weight = 170180.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.031083 restraints weight = 136640.856| |-----------------------------------------------------------------------------| r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.7770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 12911 Z= 0.402 Angle : 1.201 19.848 18166 Z= 0.535 Chirality : 0.056 0.454 2692 Planarity : 0.006 0.069 2305 Dihedral : 11.275 59.807 5093 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -2.19 (0.18), residues: 2042 helix: -0.30 (0.25), residues: 429 sheet: -1.29 (0.21), residues: 613 loop : -2.06 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.01287 ( 54) link_NAG-ASN : angle 4.37528 ( 162) link_ALPHA1-6 : bond 0.00964 ( 8) link_ALPHA1-6 : angle 3.61075 ( 24) link_BETA1-4 : bond 0.00776 ( 63) link_BETA1-4 : angle 2.90331 ( 189) link_ALPHA1-2 : bond 0.00964 ( 5) link_ALPHA1-2 : angle 2.78959 ( 15) link_ALPHA1-3 : bond 0.00825 ( 19) link_ALPHA1-3 : angle 2.47941 ( 57) hydrogen bonds : bond 0.05772 ( 634) hydrogen bonds : angle 7.51344 ( 1776) SS BOND : bond 0.00639 ( 42) SS BOND : angle 1.42682 ( 84) covalent geometry : bond 0.00682 (12720) covalent geometry : angle 1.07973 (17635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.286 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1238 time to fit residues: 9.9722 Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 157 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.036838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.030539 restraints weight = 220978.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.030988 restraints weight = 166824.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.031360 restraints weight = 133270.159| |-----------------------------------------------------------------------------| r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.7860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 12911 Z= 0.261 Angle : 0.978 19.419 18166 Z= 0.421 Chirality : 0.052 0.446 2692 Planarity : 0.005 0.069 2305 Dihedral : 10.108 59.024 5093 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -1.85 (0.18), residues: 2042 helix: 0.40 (0.25), residues: 426 sheet: -1.28 (0.21), residues: 608 loop : -1.91 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00972 ( 54) link_NAG-ASN : angle 4.02576 ( 162) link_ALPHA1-6 : bond 0.00908 ( 8) link_ALPHA1-6 : angle 3.59654 ( 24) link_BETA1-4 : bond 0.00516 ( 63) link_BETA1-4 : angle 2.36067 ( 189) link_ALPHA1-2 : bond 0.00627 ( 5) link_ALPHA1-2 : angle 2.52043 ( 15) link_ALPHA1-3 : bond 0.00846 ( 19) link_ALPHA1-3 : angle 1.93446 ( 57) hydrogen bonds : bond 0.04359 ( 634) hydrogen bonds : angle 6.57615 ( 1776) SS BOND : bond 0.00420 ( 42) SS BOND : angle 1.05106 ( 84) covalent geometry : bond 0.00453 (12720) covalent geometry : angle 0.85850 (17635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.247 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1130 time to fit residues: 9.3079 Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 7 optimal weight: 0.2980 chunk 115 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.036936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.030578 restraints weight = 221232.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.031006 restraints weight = 167059.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.031395 restraints weight = 134214.069| |-----------------------------------------------------------------------------| r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.8213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12911 Z= 0.248 Angle : 0.929 19.426 18166 Z= 0.401 Chirality : 0.051 0.476 2692 Planarity : 0.005 0.063 2305 Dihedral : 9.450 58.503 5093 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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 (0.19), residues: 2042 helix: 0.93 (0.26), residues: 426 sheet: -1.31 (0.21), residues: 596 loop : -1.96 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00950 ( 54) link_NAG-ASN : angle 3.86925 ( 162) link_ALPHA1-6 : bond 0.00820 ( 8) link_ALPHA1-6 : angle 3.01507 ( 24) link_BETA1-4 : bond 0.00498 ( 63) link_BETA1-4 : angle 2.32012 ( 189) link_ALPHA1-2 : bond 0.00630 ( 5) link_ALPHA1-2 : angle 2.38486 ( 15) link_ALPHA1-3 : bond 0.00749 ( 19) link_ALPHA1-3 : angle 1.96482 ( 57) hydrogen bonds : bond 0.04083 ( 634) hydrogen bonds : angle 6.28868 ( 1776) SS BOND : bond 0.00374 ( 42) SS BOND : angle 1.06387 ( 84) covalent geometry : bond 0.00435 (12720) covalent geometry : angle 0.81148 (17635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1102 time to fit residues: 9.1657 Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 68 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 14 optimal weight: 0.0010 chunk 194 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 overall best weight: 6.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.036476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.030247 restraints weight = 221659.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.030674 restraints weight = 167129.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.031053 restraints weight = 133924.610| |-----------------------------------------------------------------------------| r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.8610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 12911 Z= 0.321 Angle : 1.046 19.426 18166 Z= 0.459 Chirality : 0.053 0.521 2692 Planarity : 0.005 0.065 2305 Dihedral : 10.214 59.630 5093 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -2.25 (0.18), residues: 2042 helix: 0.00 (0.25), residues: 444 sheet: -1.49 (0.22), residues: 590 loop : -2.19 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.01095 ( 54) link_NAG-ASN : angle 4.06644 ( 162) link_ALPHA1-6 : bond 0.00820 ( 8) link_ALPHA1-6 : angle 3.01941 ( 24) link_BETA1-4 : bond 0.00606 ( 63) link_BETA1-4 : angle 2.56669 ( 189) link_ALPHA1-2 : bond 0.00586 ( 5) link_ALPHA1-2 : angle 2.45607 ( 15) link_ALPHA1-3 : bond 0.00725 ( 19) link_ALPHA1-3 : angle 2.18427 ( 57) hydrogen bonds : bond 0.04913 ( 634) hydrogen bonds : angle 6.95714 ( 1776) SS BOND : bond 0.00554 ( 42) SS BOND : angle 1.45207 ( 84) covalent geometry : bond 0.00558 (12720) covalent geometry : angle 0.92807 (17635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1091 time to fit residues: 8.9294 Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 102 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.036662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.030399 restraints weight = 219265.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.030854 restraints weight = 165404.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.031227 restraints weight = 131750.731| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.8724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 12911 Z= 0.263 Angle : 0.954 19.364 18166 Z= 0.413 Chirality : 0.051 0.515 2692 Planarity : 0.005 0.062 2305 Dihedral : 9.779 59.981 5093 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.14 % Favored : 89.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.18), residues: 2042 helix: 0.53 (0.25), residues: 426 sheet: -1.55 (0.22), residues: 593 loop : -2.18 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00964 ( 54) link_NAG-ASN : angle 3.89626 ( 162) link_ALPHA1-6 : bond 0.00816 ( 8) link_ALPHA1-6 : angle 2.92205 ( 24) link_BETA1-4 : bond 0.00525 ( 63) link_BETA1-4 : angle 2.36451 ( 189) link_ALPHA1-2 : bond 0.00602 ( 5) link_ALPHA1-2 : angle 2.36804 ( 15) link_ALPHA1-3 : bond 0.00681 ( 19) link_ALPHA1-3 : angle 1.98320 ( 57) hydrogen bonds : bond 0.04298 ( 634) hydrogen bonds : angle 6.56798 ( 1776) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.18751 ( 84) covalent geometry : bond 0.00464 (12720) covalent geometry : angle 0.83859 (17635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.230 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1120 time to fit residues: 9.1092 Evaluate side-chains 35 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 143 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 199 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 0.0270 chunk 136 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.036840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.030547 restraints weight = 219190.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.031003 restraints weight = 164984.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.031370 restraints weight = 131600.663| |-----------------------------------------------------------------------------| r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.8777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12911 Z= 0.208 Angle : 0.871 19.131 18166 Z= 0.373 Chirality : 0.050 0.501 2692 Planarity : 0.004 0.060 2305 Dihedral : 9.111 58.294 5093 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.19), residues: 2042 helix: 0.81 (0.25), residues: 462 sheet: -1.52 (0.22), residues: 596 loop : -1.96 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00861 ( 54) link_NAG-ASN : angle 3.72858 ( 162) link_ALPHA1-6 : bond 0.00835 ( 8) link_ALPHA1-6 : angle 2.74011 ( 24) link_BETA1-4 : bond 0.00463 ( 63) link_BETA1-4 : angle 2.21313 ( 189) link_ALPHA1-2 : bond 0.00563 ( 5) link_ALPHA1-2 : angle 2.33415 ( 15) link_ALPHA1-3 : bond 0.00657 ( 19) link_ALPHA1-3 : angle 1.81373 ( 57) hydrogen bonds : bond 0.03798 ( 634) hydrogen bonds : angle 6.14913 ( 1776) SS BOND : bond 0.00315 ( 42) SS BOND : angle 0.94030 ( 84) covalent geometry : bond 0.00369 (12720) covalent geometry : angle 0.75554 (17635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2835.94 seconds wall clock time: 50 minutes 8.43 seconds (3008.43 seconds total)