Starting phenix.real_space_refine on Wed Mar 4 10:23:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mzj_9303/03_2026/6mzj_9303.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mzj_9303/03_2026/6mzj_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 { model { file = "/net/cci-nas-00/data/ceres_data/6mzj_9303/03_2026/6mzj_9303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mzj_9303/03_2026/6mzj_9303.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mzj_9303/03_2026/6mzj_9303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mzj_9303/03_2026/6mzj_9303.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASN:plan1': 30, 'TRP:plan': 15, 'TYR:plan': 16, 'GLU:plan': 27, 'PHE:plan': 15, 'HIS:plan': 7, 'ASP:plan': 22, 'GLN:plan1': 25, 'ARG:plan': 24} 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: {'GLU:plan': 5, 'GLN:plan1': 8, 'ARG:plan': 5, 'TYR:plan': 6, 'TRP:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'PHE: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: {'PCA:plan-2': 1, 'GLN:plan1': 8, 'GLU:plan': 3, 'TYR:plan': 8, 'PHE:plan': 3, 'HIS:plan': 2, 'TRP:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 5, 'ASP:plan': 5} 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: {'ASN:plan1': 30, 'TRP:plan': 15, 'TYR:plan': 16, 'GLU:plan': 27, 'PHE:plan': 15, 'HIS:plan': 7, 'ASP:plan': 22, 'GLN:plan1': 25, 'ARG:plan': 24} 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: {'GLU:plan': 5, 'GLN:plan1': 8, 'ARG:plan': 5, 'TYR:plan': 6, 'TRP:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'PHE: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: {'PCA:plan-2': 1, 'GLN:plan1': 8, 'GLU:plan': 3, 'TYR:plan': 8, 'PHE:plan': 3, 'HIS:plan': 2, 'TRP:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 5, 'ASP:plan': 5} 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: {'ASN:plan1': 30, 'TRP:plan': 15, 'TYR:plan': 16, 'GLU:plan': 27, 'PHE:plan': 15, 'HIS:plan': 7, 'ASP:plan': 22, 'GLN:plan1': 25, 'ARG:plan': 24} 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: 3.59, per 1000 atoms: 0.28 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: 2.09 Conformation dependent library (CDL) restraints added in 571.9 milliseconds 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: 0.69 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: 1.87 Time building geometry restraints manager: 2.39 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: 0.02 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.300 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 TYR 0.000 0.000 TYR A 39 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 35 Details of bonding type rmsd covalent geometry : bond 0.01496 (12720) covalent geometry : angle 1.59431 (17635) SS BOND : bond 0.06112 ( 42) SS BOND : angle 3.99642 ( 84) hydrogen bonds : bond 0.19128 ( 634) hydrogen bonds : angle 7.92778 ( 1776) 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) 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_NAG-ASN : bond 0.02284 ( 54) link_NAG-ASN : angle 2.40898 ( 162) *********************** 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 : 0.406 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 45 average time/residue: 0.0491 time to fit residues: 4.6328 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 : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.2893 r_free = 0.2893 target = 0.041242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.034600 restraints weight = 221195.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.035039 restraints weight = 174183.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.035405 restraints weight = 143431.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.035696 restraints weight = 121563.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.035923 restraints weight = 106225.882| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12911 Z= 0.276 Angle : 1.090 23.181 18166 Z= 0.469 Chirality : 0.057 0.468 2692 Planarity : 0.005 0.031 2305 Dihedral : 12.189 83.751 5093 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.40 % Favored : 97.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2042 helix: 1.32 (0.25), residues: 396 sheet: 0.07 (0.19), residues: 635 loop : -0.20 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 39 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 35 Details of bonding type rmsd covalent geometry : bond 0.00459 (12720) covalent geometry : angle 0.94935 (17635) SS BOND : bond 0.01121 ( 42) SS BOND : angle 1.37595 ( 84) hydrogen bonds : bond 0.05260 ( 634) hydrogen bonds : angle 5.84399 ( 1776) link_ALPHA1-2 : bond 0.00558 ( 5) link_ALPHA1-2 : angle 2.23063 ( 15) link_ALPHA1-3 : bond 0.00981 ( 19) link_ALPHA1-3 : angle 3.80852 ( 57) link_ALPHA1-6 : bond 0.01583 ( 8) link_ALPHA1-6 : angle 2.98390 ( 24) link_BETA1-4 : bond 0.00644 ( 63) link_BETA1-4 : angle 2.75271 ( 189) link_NAG-ASN : bond 0.01359 ( 54) link_NAG-ASN : angle 4.27928 ( 162) *********************** 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 : 0.325 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0500 time to fit residues: 3.7842 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 : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 183 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 163 optimal weight: 30.0000 chunk 189 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 134 optimal weight: 0.0040 chunk 125 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 overall best weight: 6.0000 ------------------------------------------------------------------------------- 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 = 0.2794 r_free = 0.2794 target = 0.038441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.032124 restraints weight = 227752.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.032551 restraints weight = 174928.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.032903 restraints weight = 141712.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.033192 restraints weight = 118955.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.033426 restraints weight = 103118.681| |-----------------------------------------------------------------------------| r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 12911 Z= 0.325 Angle : 1.048 17.230 18166 Z= 0.463 Chirality : 0.054 0.473 2692 Planarity : 0.005 0.046 2305 Dihedral : 11.044 58.906 5093 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.18), residues: 2042 helix: 1.00 (0.25), residues: 423 sheet: -0.21 (0.20), residues: 639 loop : -0.75 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 39 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 35 Details of bonding type rmsd covalent geometry : bond 0.00564 (12720) covalent geometry : angle 0.93520 (17635) SS BOND : bond 0.00490 ( 42) SS BOND : angle 1.38635 ( 84) hydrogen bonds : bond 0.05642 ( 634) hydrogen bonds : angle 6.22694 ( 1776) link_ALPHA1-2 : bond 0.00466 ( 5) link_ALPHA1-2 : angle 2.10756 ( 15) link_ALPHA1-3 : bond 0.01014 ( 19) link_ALPHA1-3 : angle 1.91440 ( 57) link_ALPHA1-6 : bond 0.01405 ( 8) link_ALPHA1-6 : angle 3.50579 ( 24) link_BETA1-4 : bond 0.00590 ( 63) link_BETA1-4 : angle 2.46227 ( 189) link_NAG-ASN : bond 0.01840 ( 54) link_NAG-ASN : angle 4.05712 ( 162) *********************** 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 : 0.397 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0399 time to fit residues: 3.1657 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 : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 96 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 57 optimal weight: 30.0000 chunk 114 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.2771 r_free = 0.2771 target = 0.037806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.031700 restraints weight = 232702.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.032082 restraints weight = 183224.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.032388 restraints weight = 151037.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.032643 restraints weight = 128817.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.032875 restraints weight = 112973.102| |-----------------------------------------------------------------------------| r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 12911 Z= 0.317 Angle : 1.064 19.207 18166 Z= 0.467 Chirality : 0.055 0.491 2692 Planarity : 0.005 0.043 2305 Dihedral : 10.276 59.879 5093 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.83 % Favored : 94.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.18), residues: 2042 helix: 0.74 (0.26), residues: 411 sheet: -0.75 (0.20), residues: 646 loop : -1.30 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 39 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 35 Details of bonding type rmsd covalent geometry : bond 0.00546 (12720) covalent geometry : angle 0.94769 (17635) SS BOND : bond 0.00474 ( 42) SS BOND : angle 1.17348 ( 84) hydrogen bonds : bond 0.04839 ( 634) hydrogen bonds : angle 6.47418 ( 1776) link_ALPHA1-2 : bond 0.00655 ( 5) link_ALPHA1-2 : angle 2.66291 ( 15) link_ALPHA1-3 : bond 0.00849 ( 19) link_ALPHA1-3 : angle 2.41949 ( 57) link_ALPHA1-6 : bond 0.01237 ( 8) link_ALPHA1-6 : angle 3.22119 ( 24) link_BETA1-4 : bond 0.00601 ( 63) link_BETA1-4 : angle 2.53182 ( 189) link_NAG-ASN : bond 0.01243 ( 54) link_NAG-ASN : angle 4.08645 ( 162) *********************** 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 : 0.404 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0498 time to fit residues: 3.7929 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 : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 190 optimal weight: 0.0670 chunk 60 optimal weight: 0.0030 chunk 110 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 overall best weight: 4.2134 ------------------------------------------------------------------------------- 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 = 0.2775 r_free = 0.2775 target = 0.037861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.031706 restraints weight = 231598.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.032092 restraints weight = 181887.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.032417 restraints weight = 149816.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.032690 restraints weight = 126784.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.032886 restraints weight = 110725.713| |-----------------------------------------------------------------------------| r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.6613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 12911 Z= 0.219 Angle : 0.883 18.823 18166 Z= 0.380 Chirality : 0.051 0.451 2692 Planarity : 0.004 0.047 2305 Dihedral : 9.329 57.136 5093 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.19), residues: 2042 helix: 1.45 (0.26), residues: 411 sheet: -0.81 (0.20), residues: 646 loop : -1.28 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 39 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 35 Details of bonding type rmsd covalent geometry : bond 0.00389 (12720) covalent geometry : angle 0.76730 (17635) SS BOND : bond 0.00310 ( 42) SS BOND : angle 0.94804 ( 84) hydrogen bonds : bond 0.03993 ( 634) hydrogen bonds : angle 5.82259 ( 1776) link_ALPHA1-2 : bond 0.00536 ( 5) link_ALPHA1-2 : angle 2.31235 ( 15) link_ALPHA1-3 : bond 0.00921 ( 19) link_ALPHA1-3 : angle 1.67746 ( 57) link_ALPHA1-6 : bond 0.01131 ( 8) link_ALPHA1-6 : angle 3.28272 ( 24) link_BETA1-4 : bond 0.00468 ( 63) link_BETA1-4 : angle 2.16941 ( 189) link_NAG-ASN : bond 0.01003 ( 54) link_NAG-ASN : angle 3.77528 ( 162) *********************** 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 : 0.408 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0488 time to fit residues: 3.7679 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 : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 109 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 112 optimal weight: 0.0770 chunk 72 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 overall best weight: 5.8146 ------------------------------------------------------------------------------- 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 = 0.2735 r_free = 0.2735 target = 0.036856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.030589 restraints weight = 222780.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.031033 restraints weight = 168556.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.031382 restraints weight = 134811.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.031694 restraints weight = 112559.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.031914 restraints weight = 96601.682| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.7533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 12911 Z= 0.300 Angle : 1.042 19.449 18166 Z= 0.455 Chirality : 0.054 0.465 2692 Planarity : 0.005 0.063 2305 Dihedral : 10.174 57.753 5093 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.18), residues: 2042 helix: 0.48 (0.25), residues: 429 sheet: -1.04 (0.21), residues: 616 loop : -1.75 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 39 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 35 Details of bonding type rmsd covalent geometry : bond 0.00518 (12720) covalent geometry : angle 0.92115 (17635) SS BOND : bond 0.00600 ( 42) SS BOND : angle 1.29326 ( 84) hydrogen bonds : bond 0.04928 ( 634) hydrogen bonds : angle 6.64760 ( 1776) link_ALPHA1-2 : bond 0.00599 ( 5) link_ALPHA1-2 : angle 2.56470 ( 15) link_ALPHA1-3 : bond 0.00771 ( 19) link_ALPHA1-3 : angle 2.16238 ( 57) link_ALPHA1-6 : bond 0.00971 ( 8) link_ALPHA1-6 : angle 3.38824 ( 24) link_BETA1-4 : bond 0.00655 ( 63) link_BETA1-4 : angle 2.59955 ( 189) link_NAG-ASN : bond 0.01077 ( 54) link_NAG-ASN : angle 4.09110 ( 162) *********************** 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 : 0.425 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0464 time to fit residues: 3.6548 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 : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 71 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 159 optimal weight: 0.0470 chunk 195 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 42 optimal weight: 0.0570 overall best weight: 4.4202 ------------------------------------------------------------------------------- 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 = 0.2756 r_free = 0.2756 target = 0.037270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.030941 restraints weight = 220106.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.031360 restraints weight = 166965.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.031740 restraints weight = 134600.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.032015 restraints weight = 112719.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.032273 restraints weight = 97410.167| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.7644 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= 0.221 Angle : 0.890 18.845 18166 Z= 0.382 Chirality : 0.050 0.445 2692 Planarity : 0.004 0.063 2305 Dihedral : 9.448 59.233 5093 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.19), residues: 2042 helix: 1.14 (0.25), residues: 429 sheet: -1.06 (0.21), residues: 609 loop : -1.61 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 39 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 35 Details of bonding type rmsd covalent geometry : bond 0.00385 (12720) covalent geometry : angle 0.77440 (17635) SS BOND : bond 0.00323 ( 42) SS BOND : angle 0.88698 ( 84) hydrogen bonds : bond 0.03903 ( 634) hydrogen bonds : angle 6.02210 ( 1776) link_ALPHA1-2 : bond 0.00549 ( 5) link_ALPHA1-2 : angle 2.36658 ( 15) link_ALPHA1-3 : bond 0.00809 ( 19) link_ALPHA1-3 : angle 1.74799 ( 57) link_ALPHA1-6 : bond 0.00982 ( 8) link_ALPHA1-6 : angle 3.35555 ( 24) link_BETA1-4 : bond 0.00461 ( 63) link_BETA1-4 : angle 2.19569 ( 189) link_NAG-ASN : bond 0.00872 ( 54) link_NAG-ASN : angle 3.77402 ( 162) *********************** 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 : 0.403 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0489 time to fit residues: 3.7572 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 : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 197 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 159 optimal weight: 0.0980 chunk 97 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 163 optimal weight: 40.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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 = 0.2758 r_free = 0.2758 target = 0.037295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.030950 restraints weight = 218746.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.031376 restraints weight = 165815.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.031757 restraints weight = 133437.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.032055 restraints weight = 111570.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.032277 restraints weight = 95901.479| |-----------------------------------------------------------------------------| r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.7815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12911 Z= 0.194 Angle : 0.836 18.807 18166 Z= 0.357 Chirality : 0.049 0.457 2692 Planarity : 0.004 0.060 2305 Dihedral : 8.840 58.303 5093 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.19), residues: 2042 helix: 1.70 (0.26), residues: 426 sheet: -1.06 (0.21), residues: 609 loop : -1.54 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 39 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 35 Details of bonding type rmsd covalent geometry : bond 0.00344 (12720) covalent geometry : angle 0.71730 (17635) SS BOND : bond 0.00328 ( 42) SS BOND : angle 0.95906 ( 84) hydrogen bonds : bond 0.03572 ( 634) hydrogen bonds : angle 5.72195 ( 1776) link_ALPHA1-2 : bond 0.00502 ( 5) link_ALPHA1-2 : angle 2.31100 ( 15) link_ALPHA1-3 : bond 0.00738 ( 19) link_ALPHA1-3 : angle 1.68222 ( 57) link_ALPHA1-6 : bond 0.01002 ( 8) link_ALPHA1-6 : angle 3.20479 ( 24) link_BETA1-4 : bond 0.00433 ( 63) link_BETA1-4 : angle 2.14594 ( 189) link_NAG-ASN : bond 0.00832 ( 54) link_NAG-ASN : angle 3.66537 ( 162) *********************** 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 : 0.398 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0525 time to fit residues: 3.9667 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 : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 60 optimal weight: 20.0000 chunk 152 optimal weight: 30.0000 chunk 36 optimal weight: 0.3980 chunk 12 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 83 optimal weight: 0.3980 overall best weight: 4.1586 ------------------------------------------------------------------------------- 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 = 0.2755 r_free = 0.2755 target = 0.037238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.030913 restraints weight = 220245.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.031372 restraints weight = 166540.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.031745 restraints weight = 132521.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.032045 restraints weight = 110558.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.032276 restraints weight = 95008.398| |-----------------------------------------------------------------------------| r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.8054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 12911 Z= 0.217 Angle : 0.864 18.442 18166 Z= 0.372 Chirality : 0.050 0.484 2692 Planarity : 0.004 0.059 2305 Dihedral : 8.737 55.679 5093 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.19), residues: 2042 helix: 1.31 (0.26), residues: 444 sheet: -1.15 (0.21), residues: 609 loop : -1.56 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 39 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 35 Details of bonding type rmsd covalent geometry : bond 0.00386 (12720) covalent geometry : angle 0.74537 (17635) SS BOND : bond 0.00374 ( 42) SS BOND : angle 0.90594 ( 84) hydrogen bonds : bond 0.03781 ( 634) hydrogen bonds : angle 5.84134 ( 1776) link_ALPHA1-2 : bond 0.00507 ( 5) link_ALPHA1-2 : angle 2.28500 ( 15) link_ALPHA1-3 : bond 0.00696 ( 19) link_ALPHA1-3 : angle 1.74826 ( 57) link_ALPHA1-6 : bond 0.00958 ( 8) link_ALPHA1-6 : angle 3.28257 ( 24) link_BETA1-4 : bond 0.00449 ( 63) link_BETA1-4 : angle 2.20027 ( 189) link_NAG-ASN : bond 0.00859 ( 54) link_NAG-ASN : angle 3.75390 ( 162) *********************** 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 : 0.383 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0501 time to fit residues: 3.8016 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 180 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 177 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 146 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 overall best weight: 6.7790 ------------------------------------------------------------------------------- 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 = 0.036484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.030306 restraints weight = 222887.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.030737 restraints weight = 167074.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.031114 restraints weight = 133423.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.031414 restraints weight = 111046.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.031649 restraints weight = 94986.968| |-----------------------------------------------------------------------------| r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.8589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 12911 Z= 0.331 Angle : 1.049 18.602 18166 Z= 0.462 Chirality : 0.053 0.532 2692 Planarity : 0.005 0.062 2305 Dihedral : 9.875 56.113 5093 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.18), residues: 2042 helix: 0.26 (0.25), residues: 426 sheet: -1.27 (0.22), residues: 561 loop : -2.11 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 39 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 35 Details of bonding type rmsd covalent geometry : bond 0.00566 (12720) covalent geometry : angle 0.93196 (17635) SS BOND : bond 0.00521 ( 42) SS BOND : angle 1.35044 ( 84) hydrogen bonds : bond 0.04986 ( 634) hydrogen bonds : angle 6.88211 ( 1776) link_ALPHA1-2 : bond 0.00491 ( 5) link_ALPHA1-2 : angle 2.41275 ( 15) link_ALPHA1-3 : bond 0.00657 ( 19) link_ALPHA1-3 : angle 2.20438 ( 57) link_ALPHA1-6 : bond 0.00909 ( 8) link_ALPHA1-6 : angle 3.61881 ( 24) link_BETA1-4 : bond 0.00617 ( 63) link_BETA1-4 : angle 2.58385 ( 189) link_NAG-ASN : bond 0.01134 ( 54) link_NAG-ASN : angle 3.99399 ( 162) ********************** 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 : 0.414 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0516 time to fit residues: 3.9054 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 : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 109 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 overall best weight: 9.5990 ------------------------------------------------------------------------------- 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 = 0.2687 r_free = 0.2687 target = 0.035771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.029710 restraints weight = 225985.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.030162 restraints weight = 168942.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.030528 restraints weight = 133837.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.030824 restraints weight = 110811.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.031065 restraints weight = 94701.222| |-----------------------------------------------------------------------------| r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.9294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.138 12911 Z= 0.444 Angle : 1.275 18.622 18166 Z= 0.567 Chirality : 0.057 0.596 2692 Planarity : 0.006 0.065 2305 Dihedral : 11.615 59.923 5093 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.20 % Favored : 85.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.17), residues: 2042 helix: -1.08 (0.24), residues: 423 sheet: -1.73 (0.23), residues: 482 loop : -2.54 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 39 PHE 0.000 0.000 PHE A 53 TRP 0.000 0.000 TRP A 35 Details of bonding type rmsd covalent geometry : bond 0.00767 (12720) covalent geometry : angle 1.15447 (17635) SS BOND : bond 0.00731 ( 42) SS BOND : angle 1.68568 ( 84) hydrogen bonds : bond 0.06125 ( 634) hydrogen bonds : angle 8.09957 ( 1776) link_ALPHA1-2 : bond 0.00737 ( 5) link_ALPHA1-2 : angle 2.65026 ( 15) link_ALPHA1-3 : bond 0.00816 ( 19) link_ALPHA1-3 : angle 2.77245 ( 57) link_ALPHA1-6 : bond 0.00683 ( 8) link_ALPHA1-6 : angle 3.53269 ( 24) link_BETA1-4 : bond 0.00836 ( 63) link_BETA1-4 : angle 3.03193 ( 189) link_NAG-ASN : bond 0.01435 ( 54) link_NAG-ASN : angle 4.44980 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1391.17 seconds wall clock time: 24 minutes 43.79 seconds (1483.79 seconds total)