Starting phenix.real_space_refine on Sat Dec 9 23:55:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzj_9303/12_2023/6mzj_9303_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzj_9303/12_2023/6mzj_9303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzj_9303/12_2023/6mzj_9303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzj_9303/12_2023/6mzj_9303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzj_9303/12_2023/6mzj_9303_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzj_9303/12_2023/6mzj_9303_updated.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 85 5.16 5 C 7441 2.51 5 N 2238 2.21 5 O 2889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12653 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 2842 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 423} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Unresolved non-hydrogen bonds: 1564 Unresolved non-hydrogen angles: 2026 Unresolved non-hydrogen dihedrals: 1299 Unresolved non-hydrogen chiralities: 167 Planarities with less than four sites: {'GLN:plan1': 25, 'ARG:plan': 24, 'TYR:plan': 16, 'ASN:plan1': 30, 'TRP:plan': 15, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 27, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 856 Chain: "L" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 506 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 170 Chain: "H" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 594 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 5, 'PCA:plan-2': 1, 'ASN:plan1': 5, 'TRP:plan': 5, 'HIS:plan': 2, 'TYR:plan': 8, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 234 Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 2842 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 423} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Unresolved non-hydrogen bonds: 1564 Unresolved non-hydrogen angles: 2026 Unresolved non-hydrogen dihedrals: 1299 Unresolved non-hydrogen chiralities: 167 Planarities with less than four sites: {'GLN:plan1': 25, 'ARG:plan': 24, 'TYR:plan': 16, 'ASN:plan1': 30, 'TRP:plan': 15, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 27, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 856 Chain: "C" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 506 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 170 Chain: "D" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 594 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 5, 'PCA:plan-2': 1, 'ASN:plan1': 5, 'TRP:plan': 5, 'HIS:plan': 2, 'TYR:plan': 8, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 234 Chain: "E" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 2842 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 423} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Unresolved non-hydrogen bonds: 1564 Unresolved non-hydrogen angles: 2026 Unresolved non-hydrogen dihedrals: 1299 Unresolved non-hydrogen chiralities: 167 Planarities with less than four sites: {'GLN:plan1': 25, 'ARG:plan': 24, 'TYR:plan': 16, 'ASN:plan1': 30, 'TRP:plan': 15, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 27, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 856 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 7.89, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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: 8.06 Conformation dependent library (CDL) restraints added in 2.8 seconds 4084 Ramachandran restraints generated. 2042 Oldfield, 0 Emsley, 2042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 38 sheets defined 21.1% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 194 through 197 removed outlier: 4.191A pdb=" N ASN A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.769A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.623A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 524 through 527 Processing helix chain 'A' and resid 530 through 543 removed outlier: 4.276A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 628 through 661 removed outlier: 3.612A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASN A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N TYR A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLN A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' 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 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'B' and resid 99 through 115 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 194 through 197 removed outlier: 4.189A pdb=" N ASN B 197 " --> pdb=" O ILE B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 335 through 352 removed outlier: 3.769A pdb=" N HIS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.622A pdb=" N ARG B 480 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 524 through 527 Processing helix chain 'B' and resid 530 through 543 removed outlier: 4.275A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 628 through 661 removed outlier: 3.612A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 639 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' 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 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 194 through 197 removed outlier: 4.190A pdb=" N ASN E 197 " --> pdb=" O ILE E 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 335 through 352 removed outlier: 3.769A pdb=" N HIS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.623A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 485 No H-bonds generated for 'chain 'E' and resid 483 through 485' Processing helix chain 'E' and resid 524 through 527 Processing helix chain 'E' and resid 530 through 543 removed outlier: 4.276A pdb=" N MET E 535 " --> pdb=" O GLY E 531 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR E 536 " --> pdb=" O ALA E 532 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU E 537 " --> pdb=" O ALA E 533 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL E 539 " --> pdb=" O MET E 535 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 595 Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 628 through 661 removed outlier: 3.613A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASN E 637 " --> pdb=" O LYS E 633 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N TYR E 638 " --> pdb=" O GLU E 634 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR E 639 " --> pdb=" O ILE E 635 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLN E 640 " --> pdb=" O SER E 636 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE E 641 " --> pdb=" O ASN E 637 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 494 through 499 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, 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= E, first strand: chain 'A' and resid 130 through 132 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.315A pdb=" N ASN A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE A 468 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLN A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 414 through 417 removed outlier: 6.920A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 374 through 377 removed outlier: 3.576A pdb=" N PHE A 383 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing sheet with id= J, 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= K, 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= L, first strand: chain 'L' and resid 85 through 89 removed outlier: 5.916A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= N, first strand: chain 'H' and resid 107 through 109 removed outlier: 6.177A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 494 through 499 Processing sheet with id= P, first strand: chain 'B' and resid 45 through 47 Processing sheet with id= Q, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= R, 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= S, first strand: chain 'B' and resid 130 through 132 Processing sheet with id= T, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= U, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.315A pdb=" N ASN B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N PHE B 468 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N GLN B 362 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.920A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 374 through 377 removed outlier: 3.576A pdb=" N PHE B 383 " --> pdb=" O PHE B 376 " (cutoff:3.500A) Processing sheet with id= X, 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= Y, 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= Z, first strand: chain 'C' and resid 85 through 89 removed outlier: 5.917A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 3 through 6 Processing sheet with id= AB, first strand: chain 'D' and resid 107 through 109 removed outlier: 6.177A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA D 40 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU D 45 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 494 through 499 Processing sheet with id= AD, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= AE, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= AF, 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= AG, first strand: chain 'E' and resid 130 through 132 Processing sheet with id= AH, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AI, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.315A pdb=" N ASN E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE E 468 " --> pdb=" O ASN E 357 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLN E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 414 through 417 removed outlier: 6.919A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 374 through 377 removed outlier: 3.576A pdb=" N PHE E 383 " --> pdb=" O PHE E 376 " (cutoff:3.500A) Processing sheet with id= AL, 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) 585 hydrogen bonds defined for protein. 1557 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: 4.40 Time building geometry restraints manager: 8.39 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: 101.62 - 107.15: 603 107.15 - 112.68: 7605 112.68 - 118.21: 2736 118.21 - 123.75: 6591 123.75 - 129.28: 100 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 - 14.84: 8199 14.84 - 29.68: 216 29.68 - 44.51: 94 44.51 - 59.35: 42 59.35 - 74.19: 9 Dihedral angle restraints: 8560 sinusoidal: 2600 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 8557 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: 5361 2.86 - 3.37: 10465 3.37 - 3.88: 17496 3.88 - 4.39: 16999 4.39 - 4.90: 27895 Nonbonded interactions: 78216 Sorted by model distance: nonbonded pdb=" O3 NAG X 1 " pdb=" O5 NAG X 2 " model vdw 2.352 2.440 nonbonded pdb=" O3 NAG I 1 " pdb=" O5 NAG I 2 " model vdw 2.353 2.440 nonbonded pdb=" O3 NAG l 1 " pdb=" O5 NAG l 2 " model vdw 2.354 2.440 nonbonded pdb=" O3 NAG N 2 " pdb=" O7 NAG N 2 " model vdw 2.383 2.440 nonbonded pdb=" O3 NAG p 2 " pdb=" O7 NAG p 2 " model vdw 2.383 2.440 ... (remaining 78211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.200 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 41.700 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.850 ------------------------------------------------------------------------------- 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 : 0.015 0.085 12720 Z= 0.947 Angle : 1.594 8.593 17635 Z= 0.928 Chirality : 0.093 0.653 2692 Planarity : 0.004 0.013 2305 Dihedral : 9.301 74.189 4540 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.23 % Favored : 96.62 % Rotamer: Outliers : 2.65 % Allowed : 5.31 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2042 helix: -0.09 (0.25), residues: 405 sheet: 0.10 (0.20), residues: 620 loop : -0.13 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 *********************** 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 fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 1.390 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 45 average time/residue: 0.1193 time to fit residues: 11.5731 Evaluate side-chains 35 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 30.0000 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 83 optimal weight: 0.0170 chunk 162 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12720 Z= 0.230 Angle : 0.687 9.684 17635 Z= 0.334 Chirality : 0.050 0.576 2692 Planarity : 0.004 0.027 2305 Dihedral : 7.704 55.960 4086 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.52 % Favored : 98.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.19), residues: 2042 helix: 2.20 (0.28), residues: 396 sheet: 0.32 (0.20), residues: 657 loop : 0.13 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.279 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1151 time to fit residues: 9.4041 Evaluate side-chains 35 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.290 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 156 optimal weight: 0.0670 chunk 128 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 188 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 151 optimal weight: 9.9990 overall best weight: 4.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 12720 Z= 0.334 Angle : 0.889 12.109 17635 Z= 0.420 Chirality : 0.052 0.472 2692 Planarity : 0.005 0.044 2305 Dihedral : 8.981 59.383 4086 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.04 % Favored : 94.81 % Rotamer: Outliers : 0.44 % Allowed : 3.10 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.19), residues: 2042 helix: 1.10 (0.26), residues: 438 sheet: -0.13 (0.19), residues: 644 loop : -0.56 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 *********************** 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 36 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 1.359 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.1163 time to fit residues: 9.7779 Evaluate side-chains 36 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 1.480 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1158 time to fit residues: 1.9232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 126 optimal weight: 30.0000 chunk 188 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 12720 Z= 0.359 Angle : 0.898 10.053 17635 Z= 0.419 Chirality : 0.055 0.533 2692 Planarity : 0.005 0.042 2305 Dihedral : 9.327 59.275 4086 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.78 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2042 helix: 1.03 (0.27), residues: 405 sheet: -0.47 (0.20), residues: 629 loop : -0.97 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.455 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1194 time to fit residues: 9.8389 Evaluate side-chains 35 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 4.9990 chunk 113 optimal weight: 40.0000 chunk 2 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 102 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.7417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 12720 Z= 0.430 Angle : 1.033 10.441 17635 Z= 0.483 Chirality : 0.055 0.474 2692 Planarity : 0.006 0.048 2305 Dihedral : 10.962 59.852 4086 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.60 % Favored : 90.21 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.18), residues: 2042 helix: -0.11 (0.26), residues: 396 sheet: -1.09 (0.20), residues: 631 loop : -1.78 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.574 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1831 time to fit residues: 13.6735 Evaluate side-chains 35 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.463 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12720 Z= 0.152 Angle : 0.676 7.910 17635 Z= 0.305 Chirality : 0.048 0.371 2692 Planarity : 0.004 0.045 2305 Dihedral : 8.815 59.860 4086 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 2042 helix: 1.55 (0.27), residues: 438 sheet: -0.91 (0.20), residues: 625 loop : -1.17 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.341 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1145 time to fit residues: 9.5738 Evaluate side-chains 35 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 chunk 168 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.7475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12720 Z= 0.272 Angle : 0.762 7.914 17635 Z= 0.351 Chirality : 0.050 0.405 2692 Planarity : 0.004 0.052 2305 Dihedral : 9.150 59.167 4086 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.52 % Favored : 91.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.19), residues: 2042 helix: 1.61 (0.28), residues: 399 sheet: -1.04 (0.19), residues: 655 loop : -1.36 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.411 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1136 time to fit residues: 9.5457 Evaluate side-chains 35 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 chunk 38 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 135 optimal weight: 0.0980 chunk 98 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 156 optimal weight: 10.0000 overall best weight: 3.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.7628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12720 Z= 0.217 Angle : 0.689 7.933 17635 Z= 0.315 Chirality : 0.048 0.401 2692 Planarity : 0.004 0.052 2305 Dihedral : 8.707 59.559 4086 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.17 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 2042 helix: 1.96 (0.28), residues: 402 sheet: -1.08 (0.19), residues: 669 loop : -1.34 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.300 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1130 time to fit residues: 9.2670 Evaluate side-chains 35 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 0.8980 chunk 191 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 168 optimal weight: 0.0870 chunk 175 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.7775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12720 Z= 0.190 Angle : 0.645 7.317 17635 Z= 0.295 Chirality : 0.048 0.409 2692 Planarity : 0.004 0.054 2305 Dihedral : 8.185 59.469 4086 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.25 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.19), residues: 2042 helix: 2.16 (0.28), residues: 420 sheet: -1.04 (0.19), residues: 673 loop : -1.26 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1101 time to fit residues: 9.0975 Evaluate side-chains 35 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 206 optimal weight: 10.0000 chunk 189 optimal weight: 50.0000 chunk 164 optimal weight: 0.0030 chunk 17 optimal weight: 0.0570 chunk 126 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 overall best weight: 4.0114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.8053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12720 Z= 0.248 Angle : 0.718 8.138 17635 Z= 0.331 Chirality : 0.049 0.441 2692 Planarity : 0.004 0.054 2305 Dihedral : 8.701 59.075 4086 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.33 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 2042 helix: 1.70 (0.27), residues: 420 sheet: -1.05 (0.20), residues: 639 loop : -1.33 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 ********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.443 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1220 time to fit residues: 9.7619 Evaluate side-chains 35 residues out of total 1829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 4.9990 chunk 50 optimal weight: 30.0000 chunk 151 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 chunk 144 optimal weight: 30.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.035704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.029765 restraints weight = 229704.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.030171 restraints weight = 175976.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.030480 restraints weight = 142166.326| |-----------------------------------------------------------------------------| r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.8745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 12720 Z= 0.470 Angle : 1.041 12.386 17635 Z= 0.488 Chirality : 0.055 0.502 2692 Planarity : 0.006 0.060 2305 Dihedral : 10.783 59.591 4086 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.57 % Favored : 86.24 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.18), residues: 2042 helix: -0.10 (0.26), residues: 396 sheet: -1.40 (0.21), residues: 610 loop : -2.11 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 35 PHE 0.000 0.000 PHE A 53 TYR 0.000 0.000 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.23 seconds wall clock time: 30 minutes 2.01 seconds (1802.01 seconds total)