Starting phenix.real_space_refine on Sun Aug 24 01:17:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l87_23224/08_2025/7l87_23224.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l87_23224/08_2025/7l87_23224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l87_23224/08_2025/7l87_23224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l87_23224/08_2025/7l87_23224.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l87_23224/08_2025/7l87_23224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l87_23224/08_2025/7l87_23224.map" } resolution = 3.6 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= 0.000 sd= 0.004 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 99 5.16 5 C 9809 2.51 5 N 2631 2.21 5 O 3227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15766 Number of models: 1 Model: "" Number of chains: 53 Chain: "H" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 605 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'TRANS': 120} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 121 Planarities with less than four sites: {'UNK:plan-1': 121} Unresolved non-hydrogen planarities: 121 Chain: "L" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 515 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'TRANS': 102} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 103 Planarities with less than four sites: {'UNK:plan-1': 103} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "A" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 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: 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: "M" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "Y" 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: "Z" 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: "a" 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: "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: 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: "d" 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: "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: 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: "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: 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: "m" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.33, per 1000 atoms: 0.21 Number of scatterers: 15766 At special positions: 0 Unit cell: (130.81, 132.87, 118.45, 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 99 16.00 O 3227 8.00 N 2631 7.00 C 9809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.04 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.07 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Z 3 " - " MAN Z 4 " " BMA m 3 " - " MAN m 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 5 " " BMA m 3 " - " MAN m 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " 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 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 m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " 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 s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 355 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 160 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 355 " " NAG D 601 " - " ASN D 160 " " NAG D 602 " - " ASN D 339 " " NAG D 603 " - " ASN D 137 " " NAG E 701 " - " ASN E 611 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN C 133 " " NAG I 1 " - " ASN C 156 " " NAG J 1 " - " ASN C 197 " " NAG K 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 262 " " NAG N 1 " - " ASN C 276 " " NAG O 1 " - " ASN C 295 " " NAG P 1 " - " ASN C 301 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN C 386 " " NAG S 1 " - " ASN C 392 " " NAG T 1 " - " ASN C 448 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN A 133 " " NAG W 1 " - " ASN A 156 " " NAG X 1 " - " ASN A 197 " " NAG Y 1 " - " ASN A 234 " " NAG Z 1 " - " ASN A 262 " " NAG a 1 " - " ASN A 276 " " NAG b 1 " - " ASN A 295 " " NAG c 1 " - " ASN A 301 " " NAG d 1 " - " ASN A 332 " " NAG e 1 " - " ASN A 386 " " NAG f 1 " - " ASN A 392 " " NAG g 1 " - " ASN A 448 " " NAG h 1 " - " ASN A 88 " " NAG i 1 " - " ASN D 133 " " NAG j 1 " - " ASN D 156 " " NAG k 1 " - " ASN D 197 " " NAG l 1 " - " ASN D 234 " " NAG m 1 " - " ASN D 262 " " NAG n 1 " - " ASN D 276 " " NAG o 1 " - " ASN D 295 " " NAG p 1 " - " ASN D 301 " " NAG q 1 " - " ASN D 332 " " NAG r 1 " - " ASN D 386 " " NAG s 1 " - " ASN D 392 " " NAG t 1 " - " ASN D 448 " " NAG u 1 " - " ASN D 88 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 557.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3592 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 29.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'H' and resid 64 through 67 removed outlier: 4.429A pdb=" N UNK H 67 " --> pdb=" O UNK H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.923A pdb=" N CYS C 74 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.503A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.529A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.951A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.500A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 removed outlier: 3.803A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 596 removed outlier: 3.769A pdb=" N GLN E 575 " --> pdb=" O TRP E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.990A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 663 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.939A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.457A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.527A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.310A pdb=" N ALA B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.567A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.226A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 354 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.499A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 480 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.853A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.650A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 664 294 hydrogen bonds defined for protein. 807 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: 1.49 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2642 1.31 - 1.45: 4825 1.45 - 1.59: 8369 1.59 - 1.73: 70 1.73 - 1.87: 128 Bond restraints: 16034 Sorted by residual: bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.401 -0.075 1.10e-02 8.26e+03 4.68e+01 bond pdb=" NE ARG D 503 " pdb=" CZ ARG D 503 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.55e+01 bond pdb=" CB LEU A 129 " pdb=" CG LEU A 129 " ideal model delta sigma weight residual 1.530 1.406 0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C GLN C 170 " pdb=" O GLN C 170 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.13e-02 7.83e+03 3.75e+01 bond pdb=" NE1 TRP E 631 " pdb=" CE2 TRP E 631 " ideal model delta sigma weight residual 1.370 1.307 0.063 1.10e-02 8.26e+03 3.29e+01 ... (remaining 16029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 20987 4.04 - 8.08: 797 8.08 - 12.12: 23 12.12 - 16.16: 4 16.16 - 20.20: 2 Bond angle restraints: 21813 Sorted by residual: angle pdb=" C ASN D 137 " pdb=" N ILE D 138 " pdb=" CA ILE D 138 " ideal model delta sigma weight residual 120.98 134.88 -13.90 1.36e+00 5.41e-01 1.04e+02 angle pdb=" N ILE A 184 " pdb=" CA ILE A 184 " pdb=" C ILE A 184 " ideal model delta sigma weight residual 110.62 119.23 -8.61 1.02e+00 9.61e-01 7.13e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 127.21 -7.65 1.02e+00 9.61e-01 5.62e+01 angle pdb=" C CYS D 239 " pdb=" N PRO D 240 " pdb=" CA PRO D 240 " ideal model delta sigma weight residual 119.56 127.15 -7.59 1.02e+00 9.61e-01 5.53e+01 angle pdb=" N LEU B 544 " pdb=" CA LEU B 544 " pdb=" C LEU B 544 " ideal model delta sigma weight residual 110.48 99.70 10.78 1.48e+00 4.57e-01 5.31e+01 ... (remaining 21808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 10589 21.62 - 43.24: 246 43.24 - 64.86: 57 64.86 - 86.48: 51 86.48 - 108.10: 25 Dihedral angle restraints: 10968 sinusoidal: 5453 harmonic: 5515 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.79 -57.79 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 148.90 -55.90 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 145.47 -52.47 1 1.00e+01 1.00e-02 3.75e+01 ... (remaining 10965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 2236 0.171 - 0.341: 447 0.341 - 0.511: 124 0.511 - 0.682: 4 0.682 - 0.852: 2 Chirality restraints: 2813 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.45e+02 chirality pdb=" C1 NAG l 2 " pdb=" O4 NAG l 1 " pdb=" C2 NAG l 2 " pdb=" O5 NAG l 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.63e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.49e+02 ... (remaining 2810 not shown) Planarity restraints: 2711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.351 2.00e-02 2.50e+03 3.03e-01 1.14e+03 pdb=" C7 NAG M 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.086 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " 0.347 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG O 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 604 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.11e+03 pdb=" C7 NAG A 604 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A 604 " -0.068 2.00e-02 2.50e+03 pdb=" N2 NAG A 604 " 0.525 2.00e-02 2.50e+03 pdb=" O7 NAG A 604 " -0.193 2.00e-02 2.50e+03 ... (remaining 2708 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 114 2.60 - 3.18: 13733 3.18 - 3.75: 22445 3.75 - 4.33: 33799 4.33 - 4.90: 51935 Nonbonded interactions: 122026 Sorted by model distance: nonbonded pdb=" NZ LYS A 502 " pdb=" O ASP F 664 " model vdw 2.027 3.120 nonbonded pdb=" O4 MAN M 4 " pdb=" O6 MAN M 4 " model vdw 2.308 3.040 nonbonded pdb=" O PHE E 522 " pdb=" NE2 GLN E 540 " model vdw 2.312 3.120 nonbonded pdb=" O SER D 463 " pdb=" OG SER D 463 " model vdw 2.354 3.040 nonbonded pdb=" OD2 ASP A 167 " pdb=" NZ LYS A 168 " model vdw 2.408 3.120 ... (remaining 122021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 603) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' } ncs_group { reference = (chain 'H' and resid 19 through 121) selection = chain 'L' } ncs_group { reference = chain 'Q' selection = chain 'd' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'm' } 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.023 0.132 16169 Z= 1.224 Angle : 1.810 20.202 22185 Z= 1.101 Chirality : 0.152 0.852 2813 Planarity : 0.016 0.303 2659 Dihedral : 12.583 108.101 7277 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.74 (0.19), residues: 1635 helix: 0.10 (0.24), residues: 399 sheet: 1.15 (0.28), residues: 312 loop : 0.60 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 166 TYR 0.036 0.007 TYR A 384 PHE 0.052 0.006 PHE A 159 TRP 0.046 0.008 TRP C 96 HIS 0.018 0.003 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.02255 (16034) covalent geometry : angle 1.76002 (21813) SS BOND : bond 0.00949 ( 33) SS BOND : angle 3.01211 ( 66) hydrogen bonds : bond 0.19611 ( 294) hydrogen bonds : angle 6.33812 ( 807) link_ALPHA1-3 : bond 0.06747 ( 3) link_ALPHA1-3 : angle 4.00087 ( 9) link_ALPHA1-6 : bond 0.05591 ( 2) link_ALPHA1-6 : angle 3.67510 ( 6) link_BETA1-4 : bond 0.06844 ( 45) link_BETA1-4 : angle 4.80772 ( 135) link_NAG-ASN : bond 0.07224 ( 52) link_NAG-ASN : angle 2.74403 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 ASP cc_start: 0.8007 (m-30) cc_final: 0.7650 (m-30) REVERT: C 198 THR cc_start: 0.8988 (p) cc_final: 0.8633 (p) REVERT: B 632 ASP cc_start: 0.8295 (t70) cc_final: 0.8036 (t0) REVERT: B 652 GLN cc_start: 0.7855 (mt0) cc_final: 0.7515 (mt0) REVERT: B 660 LEU cc_start: 0.8970 (mt) cc_final: 0.8747 (tt) REVERT: D 122 LEU cc_start: 0.8864 (mt) cc_final: 0.8606 (mp) REVERT: F 590 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8683 (mm110) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.1245 time to fit residues: 73.1614 Evaluate side-chains 182 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 363 GLN C 425 ASN A 99 ASN A 428 GLN D 352 HIS F 543 ASN F 570 HIS F 651 ASN F 653 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113603 restraints weight = 27428.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116587 restraints weight = 15320.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118578 restraints weight = 10349.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119893 restraints weight = 7908.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120795 restraints weight = 6528.112| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16169 Z= 0.166 Angle : 0.771 14.493 22185 Z= 0.356 Chirality : 0.047 0.242 2813 Planarity : 0.004 0.048 2659 Dihedral : 9.922 83.428 4112 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.94 % Allowed : 8.43 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.17 (0.21), residues: 1635 helix: 1.60 (0.27), residues: 402 sheet: 1.22 (0.26), residues: 345 loop : 0.30 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 588 TYR 0.010 0.001 TYR D 384 PHE 0.014 0.002 PHE C 159 TRP 0.020 0.002 TRP E 571 HIS 0.009 0.001 HIS F 570 Details of bonding type rmsd covalent geometry : bond 0.00363 (16034) covalent geometry : angle 0.70644 (21813) SS BOND : bond 0.00273 ( 33) SS BOND : angle 1.01976 ( 66) hydrogen bonds : bond 0.07070 ( 294) hydrogen bonds : angle 4.34025 ( 807) link_ALPHA1-3 : bond 0.01087 ( 3) link_ALPHA1-3 : angle 2.79010 ( 9) link_ALPHA1-6 : bond 0.00869 ( 2) link_ALPHA1-6 : angle 1.71830 ( 6) link_BETA1-4 : bond 0.00677 ( 45) link_BETA1-4 : angle 2.68815 ( 135) link_NAG-ASN : bond 0.00478 ( 52) link_NAG-ASN : angle 2.72403 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 475 MET cc_start: 0.8032 (mmm) cc_final: 0.7813 (mmm) REVERT: E 634 GLU cc_start: 0.8028 (tt0) cc_final: 0.7801 (mt-10) REVERT: A 72 HIS cc_start: 0.6526 (p-80) cc_final: 0.6325 (p-80) REVERT: A 246 GLN cc_start: 0.6971 (tp-100) cc_final: 0.6640 (tp-100) REVERT: A 384 TYR cc_start: 0.8909 (m-80) cc_final: 0.8701 (m-80) REVERT: D 150 MET cc_start: 0.7762 (mmp) cc_final: 0.7407 (mmt) REVERT: D 308 ARG cc_start: 0.7540 (mmt180) cc_final: 0.7324 (mmt-90) REVERT: D 434 MET cc_start: 0.8074 (ttp) cc_final: 0.7865 (ttt) outliers start: 29 outliers final: 19 residues processed: 257 average time/residue: 0.1119 time to fit residues: 43.1105 Evaluate side-chains 193 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 80 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 157 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 425 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN D 80 ASN F 543 ASN F 570 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108592 restraints weight = 28516.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111520 restraints weight = 15655.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113486 restraints weight = 10502.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114830 restraints weight = 7978.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115641 restraints weight = 6546.276| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16169 Z= 0.167 Angle : 0.669 8.674 22185 Z= 0.315 Chirality : 0.046 0.253 2813 Planarity : 0.004 0.047 2659 Dihedral : 8.411 78.947 4112 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.28 % Allowed : 9.37 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.98 (0.21), residues: 1635 helix: 1.66 (0.27), residues: 402 sheet: 1.17 (0.27), residues: 348 loop : 0.02 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 151 TYR 0.013 0.001 TYR D 173 PHE 0.022 0.002 PHE A 159 TRP 0.015 0.001 TRP E 571 HIS 0.006 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00383 (16034) covalent geometry : angle 0.62610 (21813) SS BOND : bond 0.00338 ( 33) SS BOND : angle 0.94477 ( 66) hydrogen bonds : bond 0.05642 ( 294) hydrogen bonds : angle 4.04570 ( 807) link_ALPHA1-3 : bond 0.01074 ( 3) link_ALPHA1-3 : angle 2.01945 ( 9) link_ALPHA1-6 : bond 0.01161 ( 2) link_ALPHA1-6 : angle 1.84518 ( 6) link_BETA1-4 : bond 0.00627 ( 45) link_BETA1-4 : angle 2.09385 ( 135) link_NAG-ASN : bond 0.00307 ( 52) link_NAG-ASN : angle 2.07396 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 150 MET cc_start: 0.8780 (mtp) cc_final: 0.8356 (mtt) REVERT: C 435 TYR cc_start: 0.8582 (t80) cc_final: 0.8342 (t80) REVERT: E 617 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7830 (mtp180) REVERT: A 246 GLN cc_start: 0.7144 (tp-100) cc_final: 0.6820 (tp-100) REVERT: B 520 LEU cc_start: 0.8222 (mm) cc_final: 0.7760 (mt) REVERT: B 654 GLU cc_start: 0.7773 (tp30) cc_final: 0.7569 (tp30) REVERT: D 46 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8139 (ptpt) REVERT: D 308 ARG cc_start: 0.7568 (mmt180) cc_final: 0.7317 (mmt-90) REVERT: D 434 MET cc_start: 0.8060 (ttp) cc_final: 0.7696 (ttt) REVERT: F 542 ARG cc_start: 0.8857 (ptp90) cc_final: 0.8578 (ptt180) outliers start: 49 outliers final: 31 residues processed: 225 average time/residue: 0.1034 time to fit residues: 35.4782 Evaluate side-chains 192 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 171 optimal weight: 0.0060 chunk 112 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS D 80 ASN F 543 ASN F 570 HIS F 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107934 restraints weight = 27839.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110814 restraints weight = 15905.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112741 restraints weight = 10966.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113964 restraints weight = 8457.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114878 restraints weight = 7091.378| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16169 Z= 0.175 Angle : 0.655 10.846 22185 Z= 0.306 Chirality : 0.045 0.268 2813 Planarity : 0.003 0.045 2659 Dihedral : 7.561 74.327 4112 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.01 % Allowed : 10.58 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.85 (0.21), residues: 1635 helix: 1.76 (0.27), residues: 402 sheet: 1.02 (0.27), residues: 351 loop : -0.16 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 588 TYR 0.012 0.001 TYR D 173 PHE 0.022 0.002 PHE A 159 TRP 0.014 0.001 TRP B 623 HIS 0.026 0.002 HIS F 570 Details of bonding type rmsd covalent geometry : bond 0.00409 (16034) covalent geometry : angle 0.61123 (21813) SS BOND : bond 0.00366 ( 33) SS BOND : angle 1.62952 ( 66) hydrogen bonds : bond 0.05278 ( 294) hydrogen bonds : angle 3.82478 ( 807) link_ALPHA1-3 : bond 0.01088 ( 3) link_ALPHA1-3 : angle 2.28376 ( 9) link_ALPHA1-6 : bond 0.01119 ( 2) link_ALPHA1-6 : angle 1.94170 ( 6) link_BETA1-4 : bond 0.00594 ( 45) link_BETA1-4 : angle 1.92527 ( 135) link_NAG-ASN : bond 0.00262 ( 52) link_NAG-ASN : angle 2.01476 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: E 584 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8412 (mt-10) REVERT: A 92 GLU cc_start: 0.7801 (tp30) cc_final: 0.7355 (mm-30) REVERT: A 268 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7471 (mm-30) REVERT: D 46 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8499 (ptpt) REVERT: D 137 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.7013 (m-40) REVERT: D 434 MET cc_start: 0.8060 (ttp) cc_final: 0.7630 (ttt) outliers start: 45 outliers final: 30 residues processed: 203 average time/residue: 0.1067 time to fit residues: 33.2190 Evaluate side-chains 184 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 110 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN F 543 ASN F 570 HIS F 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.106727 restraints weight = 27977.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109612 restraints weight = 16102.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111570 restraints weight = 11109.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112839 restraints weight = 8573.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113699 restraints weight = 7161.411| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16169 Z= 0.187 Angle : 0.649 8.247 22185 Z= 0.303 Chirality : 0.045 0.251 2813 Planarity : 0.003 0.043 2659 Dihedral : 7.275 70.945 4112 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.21 % Allowed : 11.24 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.82 (0.21), residues: 1635 helix: 2.01 (0.27), residues: 384 sheet: 0.94 (0.28), residues: 348 loop : -0.24 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 617 TYR 0.023 0.001 TYR C 486 PHE 0.023 0.002 PHE A 159 TRP 0.017 0.001 TRP E 571 HIS 0.007 0.001 HIS F 570 Details of bonding type rmsd covalent geometry : bond 0.00442 (16034) covalent geometry : angle 0.60873 (21813) SS BOND : bond 0.00415 ( 33) SS BOND : angle 1.50572 ( 66) hydrogen bonds : bond 0.05260 ( 294) hydrogen bonds : angle 3.80421 ( 807) link_ALPHA1-3 : bond 0.01097 ( 3) link_ALPHA1-3 : angle 2.21972 ( 9) link_ALPHA1-6 : bond 0.01100 ( 2) link_ALPHA1-6 : angle 1.87422 ( 6) link_BETA1-4 : bond 0.00539 ( 45) link_BETA1-4 : angle 1.84135 ( 135) link_NAG-ASN : bond 0.00269 ( 52) link_NAG-ASN : angle 1.95402 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: C 434 MET cc_start: 0.8647 (ttp) cc_final: 0.8423 (ttm) REVERT: C 435 TYR cc_start: 0.8649 (t80) cc_final: 0.8422 (t80) REVERT: A 268 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 584 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7603 (mp0) REVERT: D 46 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8550 (ptpt) REVERT: D 137 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.7012 (m-40) REVERT: D 434 MET cc_start: 0.8144 (ttp) cc_final: 0.7858 (ttt) REVERT: D 475 MET cc_start: 0.8648 (mmt) cc_final: 0.8378 (mmp) outliers start: 48 outliers final: 34 residues processed: 199 average time/residue: 0.1086 time to fit residues: 32.6930 Evaluate side-chains 182 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 145 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 160 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN F 543 ASN F 570 HIS F 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103618 restraints weight = 28237.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106418 restraints weight = 16439.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108255 restraints weight = 11429.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109531 restraints weight = 8912.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110386 restraints weight = 7454.852| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16169 Z= 0.268 Angle : 0.747 7.586 22185 Z= 0.350 Chirality : 0.048 0.258 2813 Planarity : 0.004 0.041 2659 Dihedral : 7.603 68.172 4112 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.95 % Allowed : 11.58 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.20 (0.21), residues: 1635 helix: 1.62 (0.26), residues: 402 sheet: 0.41 (0.27), residues: 363 loop : -0.70 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 588 TYR 0.018 0.002 TYR C 217 PHE 0.028 0.002 PHE A 159 TRP 0.022 0.002 TRP E 571 HIS 0.029 0.002 HIS F 570 Details of bonding type rmsd covalent geometry : bond 0.00637 (16034) covalent geometry : angle 0.70629 (21813) SS BOND : bond 0.00537 ( 33) SS BOND : angle 1.64595 ( 66) hydrogen bonds : bond 0.05779 ( 294) hydrogen bonds : angle 3.99329 ( 807) link_ALPHA1-3 : bond 0.01087 ( 3) link_ALPHA1-3 : angle 2.38045 ( 9) link_ALPHA1-6 : bond 0.01023 ( 2) link_ALPHA1-6 : angle 1.76401 ( 6) link_BETA1-4 : bond 0.00567 ( 45) link_BETA1-4 : angle 1.96881 ( 135) link_NAG-ASN : bond 0.00305 ( 52) link_NAG-ASN : angle 2.13709 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 156 time to evaluate : 0.389 Fit side-chains REVERT: A 185 ASN cc_start: 0.7104 (t0) cc_final: 0.6409 (p0) REVERT: A 202 THR cc_start: 0.9109 (m) cc_final: 0.8739 (p) REVERT: A 268 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7707 (mm-30) REVERT: B 584 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7684 (mp0) REVERT: D 46 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8630 (ptpt) REVERT: D 137 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.7099 (m-40) REVERT: D 308 ARG cc_start: 0.7439 (mmt180) cc_final: 0.6977 (mmt-90) REVERT: D 434 MET cc_start: 0.8161 (ttp) cc_final: 0.7879 (ttt) REVERT: D 475 MET cc_start: 0.8780 (mmt) cc_final: 0.8517 (mmp) outliers start: 59 outliers final: 36 residues processed: 201 average time/residue: 0.1186 time to fit residues: 35.5141 Evaluate side-chains 187 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 8 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 155 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 99 ASN C 289 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN A 258 GLN D 302 ASN F 543 ASN F 570 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108173 restraints weight = 27568.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111053 restraints weight = 15738.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113009 restraints weight = 10785.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114315 restraints weight = 8287.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115110 restraints weight = 6865.212| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16169 Z= 0.113 Angle : 0.596 8.300 22185 Z= 0.280 Chirality : 0.043 0.237 2813 Planarity : 0.003 0.041 2659 Dihedral : 6.837 60.759 4112 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.28 % Allowed : 13.52 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.67 (0.21), residues: 1635 helix: 2.31 (0.27), residues: 381 sheet: 0.36 (0.25), residues: 420 loop : -0.36 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 617 TYR 0.011 0.001 TYR A 191 PHE 0.014 0.001 PHE A 159 TRP 0.013 0.001 TRP E 571 HIS 0.016 0.001 HIS F 570 Details of bonding type rmsd covalent geometry : bond 0.00254 (16034) covalent geometry : angle 0.55660 (21813) SS BOND : bond 0.00498 ( 33) SS BOND : angle 1.80042 ( 66) hydrogen bonds : bond 0.04749 ( 294) hydrogen bonds : angle 3.66247 ( 807) link_ALPHA1-3 : bond 0.01107 ( 3) link_ALPHA1-3 : angle 2.10634 ( 9) link_ALPHA1-6 : bond 0.01004 ( 2) link_ALPHA1-6 : angle 1.44441 ( 6) link_BETA1-4 : bond 0.00517 ( 45) link_BETA1-4 : angle 1.66027 ( 135) link_NAG-ASN : bond 0.00239 ( 52) link_NAG-ASN : angle 1.77578 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.579 Fit side-chains REVERT: C 82 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7605 (pm20) REVERT: E 540 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8354 (mp10) REVERT: A 37 THR cc_start: 0.9072 (m) cc_final: 0.8751 (p) REVERT: A 92 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7336 (mm-30) REVERT: A 207 LYS cc_start: 0.7793 (pttt) cc_final: 0.7339 (tmmt) REVERT: A 268 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 602 LEU cc_start: 0.8504 (mt) cc_final: 0.8269 (mt) REVERT: D 46 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8531 (ptpp) REVERT: D 150 MET cc_start: 0.7110 (mmt) cc_final: 0.6859 (mmt) REVERT: D 308 ARG cc_start: 0.7372 (mmt180) cc_final: 0.6956 (mmt-90) REVERT: D 434 MET cc_start: 0.8120 (ttp) cc_final: 0.7871 (ttt) REVERT: D 475 MET cc_start: 0.8634 (mmt) cc_final: 0.8340 (mmp) REVERT: F 536 THR cc_start: 0.8715 (p) cc_final: 0.8485 (t) REVERT: F 542 ARG cc_start: 0.8920 (ptp90) cc_final: 0.8610 (ptt180) outliers start: 34 outliers final: 20 residues processed: 196 average time/residue: 0.1149 time to fit residues: 33.6054 Evaluate side-chains 176 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 71 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 99 ASN C 289 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS D 80 ASN D 302 ASN F 543 ASN F 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105318 restraints weight = 28136.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108156 restraints weight = 16171.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110043 restraints weight = 11114.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111221 restraints weight = 8615.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112114 restraints weight = 7234.409| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16169 Z= 0.211 Angle : 0.678 7.211 22185 Z= 0.317 Chirality : 0.045 0.236 2813 Planarity : 0.004 0.040 2659 Dihedral : 6.913 55.090 4112 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.21 % Allowed : 13.65 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.38 (0.21), residues: 1635 helix: 2.06 (0.27), residues: 384 sheet: 0.26 (0.25), residues: 420 loop : -0.60 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 151 TYR 0.010 0.001 TYR D 191 PHE 0.022 0.002 PHE A 159 TRP 0.015 0.001 TRP E 571 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00502 (16034) covalent geometry : angle 0.63870 (21813) SS BOND : bond 0.00472 ( 33) SS BOND : angle 1.62588 ( 66) hydrogen bonds : bond 0.05148 ( 294) hydrogen bonds : angle 3.78404 ( 807) link_ALPHA1-3 : bond 0.01067 ( 3) link_ALPHA1-3 : angle 2.18391 ( 9) link_ALPHA1-6 : bond 0.00883 ( 2) link_ALPHA1-6 : angle 1.43035 ( 6) link_BETA1-4 : bond 0.00537 ( 45) link_BETA1-4 : angle 1.80313 ( 135) link_NAG-ASN : bond 0.00261 ( 52) link_NAG-ASN : angle 2.03125 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.392 Fit side-chains REVERT: C 136 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7330 (m-40) REVERT: C 265 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7880 (mt) REVERT: C 435 TYR cc_start: 0.8724 (t80) cc_final: 0.8524 (t80) REVERT: A 202 THR cc_start: 0.9070 (m) cc_final: 0.8831 (m) REVERT: A 268 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 520 LEU cc_start: 0.8000 (mm) cc_final: 0.7623 (mt) REVERT: B 602 LEU cc_start: 0.8541 (mt) cc_final: 0.8295 (mt) REVERT: D 46 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8549 (ptpp) REVERT: D 137 ASN cc_start: 0.7337 (OUTLIER) cc_final: 0.7077 (m-40) REVERT: D 150 MET cc_start: 0.7177 (mmt) cc_final: 0.6904 (mmt) REVERT: D 308 ARG cc_start: 0.7435 (mmt180) cc_final: 0.7026 (mmt-90) REVERT: D 434 MET cc_start: 0.8205 (ttp) cc_final: 0.7953 (ttt) REVERT: D 475 MET cc_start: 0.8733 (mmt) cc_final: 0.8426 (mmp) REVERT: F 536 THR cc_start: 0.8771 (p) cc_final: 0.8515 (t) REVERT: F 542 ARG cc_start: 0.8977 (ptp90) cc_final: 0.8689 (ptt180) REVERT: F 661 LEU cc_start: 0.9223 (mm) cc_final: 0.9013 (mt) outliers start: 48 outliers final: 34 residues processed: 201 average time/residue: 0.1112 time to fit residues: 33.8542 Evaluate side-chains 194 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 352 HIS Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 1 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 289 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS B 543 ASN D 80 ASN F 543 ASN F 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101302 restraints weight = 28609.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104030 restraints weight = 16697.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105855 restraints weight = 11630.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106996 restraints weight = 9084.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107852 restraints weight = 7677.158| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 16169 Z= 0.355 Angle : 0.876 10.222 22185 Z= 0.409 Chirality : 0.051 0.232 2813 Planarity : 0.005 0.054 2659 Dihedral : 7.837 58.920 4112 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.55 % Allowed : 13.45 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.44 (0.20), residues: 1635 helix: 1.47 (0.26), residues: 384 sheet: -0.11 (0.27), residues: 369 loop : -1.20 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 151 TYR 0.017 0.002 TYR D 173 PHE 0.035 0.003 PHE A 159 TRP 0.031 0.002 TRP E 571 HIS 0.008 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00845 (16034) covalent geometry : angle 0.83104 (21813) SS BOND : bond 0.00728 ( 33) SS BOND : angle 2.05940 ( 66) hydrogen bonds : bond 0.06381 ( 294) hydrogen bonds : angle 4.27315 ( 807) link_ALPHA1-3 : bond 0.01142 ( 3) link_ALPHA1-3 : angle 2.40174 ( 9) link_ALPHA1-6 : bond 0.00854 ( 2) link_ALPHA1-6 : angle 1.41993 ( 6) link_BETA1-4 : bond 0.00616 ( 45) link_BETA1-4 : angle 2.16930 ( 135) link_NAG-ASN : bond 0.00401 ( 52) link_NAG-ASN : angle 2.48948 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 145 time to evaluate : 0.554 Fit side-chains REVERT: C 136 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7499 (m-40) REVERT: E 543 ASN cc_start: 0.8975 (OUTLIER) cc_final: 0.8749 (m110) REVERT: A 92 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: A 185 ASN cc_start: 0.7220 (t0) cc_final: 0.6490 (p0) REVERT: A 268 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7758 (mm-30) REVERT: B 520 LEU cc_start: 0.8096 (mm) cc_final: 0.7708 (mt) REVERT: D 137 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.7296 (m-40) REVERT: D 308 ARG cc_start: 0.7500 (mmt180) cc_final: 0.7111 (mmt-90) REVERT: D 434 MET cc_start: 0.8220 (ttp) cc_final: 0.7971 (ttt) REVERT: D 475 MET cc_start: 0.8921 (mmt) cc_final: 0.8616 (mmp) REVERT: F 536 THR cc_start: 0.8879 (p) cc_final: 0.8676 (t) outliers start: 53 outliers final: 36 residues processed: 189 average time/residue: 0.1044 time to fit residues: 29.9609 Evaluate side-chains 181 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 543 ASN Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 127 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 19 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106630 restraints weight = 27849.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109476 restraints weight = 15983.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111394 restraints weight = 10971.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112696 restraints weight = 8429.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113544 restraints weight = 6978.344| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16169 Z= 0.126 Angle : 0.640 8.444 22185 Z= 0.300 Chirality : 0.043 0.193 2813 Planarity : 0.003 0.041 2659 Dihedral : 6.839 51.342 4112 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.74 % Allowed : 15.66 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.05 (0.21), residues: 1635 helix: 2.04 (0.27), residues: 384 sheet: 0.04 (0.26), residues: 402 loop : -0.93 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 151 TYR 0.012 0.001 TYR D 191 PHE 0.015 0.001 PHE A 159 TRP 0.014 0.001 TRP C 338 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00286 (16034) covalent geometry : angle 0.59756 (21813) SS BOND : bond 0.00439 ( 33) SS BOND : angle 1.74946 ( 66) hydrogen bonds : bond 0.04973 ( 294) hydrogen bonds : angle 3.80857 ( 807) link_ALPHA1-3 : bond 0.01031 ( 3) link_ALPHA1-3 : angle 2.04216 ( 9) link_ALPHA1-6 : bond 0.00871 ( 2) link_ALPHA1-6 : angle 1.59287 ( 6) link_BETA1-4 : bond 0.00520 ( 45) link_BETA1-4 : angle 1.74155 ( 135) link_NAG-ASN : bond 0.00216 ( 52) link_NAG-ASN : angle 2.01687 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.571 Fit side-chains REVERT: A 92 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: A 185 ASN cc_start: 0.7091 (t0) cc_final: 0.6398 (p0) REVERT: D 137 ASN cc_start: 0.7477 (OUTLIER) cc_final: 0.7253 (m-40) REVERT: D 178 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7789 (ttm170) REVERT: D 308 ARG cc_start: 0.7398 (mmt180) cc_final: 0.7006 (mmt-90) REVERT: D 352 HIS cc_start: 0.7633 (m90) cc_final: 0.7380 (m90) REVERT: D 434 MET cc_start: 0.8153 (ttp) cc_final: 0.7922 (ttt) REVERT: D 475 MET cc_start: 0.8733 (mmt) cc_final: 0.8446 (mmp) REVERT: F 542 ARG cc_start: 0.8899 (ptp90) cc_final: 0.8594 (ptt180) outliers start: 26 outliers final: 19 residues processed: 184 average time/residue: 0.1177 time to fit residues: 31.6892 Evaluate side-chains 169 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.121682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104153 restraints weight = 28097.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106934 restraints weight = 16273.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108810 restraints weight = 11267.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110080 restraints weight = 8735.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110957 restraints weight = 7274.119| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16169 Z= 0.221 Angle : 0.715 10.882 22185 Z= 0.332 Chirality : 0.046 0.229 2813 Planarity : 0.004 0.040 2659 Dihedral : 6.928 48.796 4112 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.21 % Allowed : 15.66 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.15 (0.21), residues: 1635 helix: 1.95 (0.27), residues: 384 sheet: 0.00 (0.27), residues: 387 loop : -1.13 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 151 TYR 0.013 0.002 TYR D 173 PHE 0.024 0.002 PHE A 159 TRP 0.017 0.002 TRP E 571 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00527 (16034) covalent geometry : angle 0.67386 (21813) SS BOND : bond 0.00499 ( 33) SS BOND : angle 1.79638 ( 66) hydrogen bonds : bond 0.05374 ( 294) hydrogen bonds : angle 3.96298 ( 807) link_ALPHA1-3 : bond 0.01006 ( 3) link_ALPHA1-3 : angle 2.07766 ( 9) link_ALPHA1-6 : bond 0.00866 ( 2) link_ALPHA1-6 : angle 1.75359 ( 6) link_BETA1-4 : bond 0.00544 ( 45) link_BETA1-4 : angle 1.86511 ( 135) link_NAG-ASN : bond 0.00261 ( 52) link_NAG-ASN : angle 2.10568 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2000.92 seconds wall clock time: 35 minutes 38.31 seconds (2138.31 seconds total)