Starting phenix.real_space_refine on Fri Sep 19 10:03:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mib_48287/09_2025/9mib_48287.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mib_48287/09_2025/9mib_48287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mib_48287/09_2025/9mib_48287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mib_48287/09_2025/9mib_48287.map" model { file = "/net/cci-nas-00/data/ceres_data/9mib_48287/09_2025/9mib_48287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mib_48287/09_2025/9mib_48287.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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 156 5.16 5 C 15813 2.51 5 N 4233 2.21 5 O 5064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25266 Number of models: 1 Model: "" Number of chains: 54 Chain: "G" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3500 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "L" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 96} Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "C" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3500 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "K" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "N" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 96} Chain: "O" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "Q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "E" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3500 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "P" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "R" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 96} 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: 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: "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: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "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: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: "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: 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: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 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: 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: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: "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: "A" 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: "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: 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: "D" 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: "E" 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: 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 Time building chain proxies: 7.31, per 1000 atoms: 0.29 Number of scatterers: 25266 At special positions: 0 Unit cell: (138.543, 145.78, 150.949, 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 156 16.00 O 5064 8.00 N 4233 7.00 C 15813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=1.49 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.07 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 100C" distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=1.49 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.07 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 98 " - pdb=" SG CYS K 100C" distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=1.49 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.08 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 98 " - pdb=" SG CYS P 100C" distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 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 Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 5 " " BMA i 3 " - " MAN i 4 " " MAN i 4 " - " MAN i 5 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 5 " ALPHA1-6 " BMA Y 3 " - " MAN Y 6 " " BMA i 3 " - " MAN i 6 " " BMA s 3 " - " MAN s 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 339 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 339 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 339 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG S 1 " - " ASN A 160 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 295 " " NAG V 1 " - " ASN A 88 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN A 301 " " NAG a 1 " - " ASN A 332 " " NAG b 1 " - " ASN A 363 " " NAG c 1 " - " ASN C 160 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 295 " " NAG f 1 " - " ASN C 88 " " NAG g 1 " - " ASN C 392 " " NAG h 1 " - " ASN C 448 " " NAG i 1 " - " ASN C 262 " " NAG j 1 " - " ASN C 301 " " NAG k 1 " - " ASN C 332 " " NAG l 1 " - " ASN C 363 " " NAG m 1 " - " ASN E 160 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 295 " " NAG p 1 " - " ASN E 88 " " NAG q 1 " - " ASN E 392 " " NAG r 1 " - " ASN E 448 " " NAG s 1 " - " ASN E 262 " " NAG t 1 " - " ASN E 301 " " NAG u 1 " - " ASN E 332 " " NAG v 1 " - " ASN E 363 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 69 sheets defined 17.5% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.563A pdb=" N LYS G 64 " --> pdb=" O ASP G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.605A pdb=" N THR G 87 " --> pdb=" O ASP G 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.925A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.544A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.790A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.903A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.500A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.835A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.240A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.563A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.604A pdb=" N THR J 87 " --> pdb=" O ASP J 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.925A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.545A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.790A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.156A 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 390 Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.903A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.501A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 649 removed outlier: 3.834A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.240A pdb=" N ILE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.563A pdb=" N LYS O 64 " --> pdb=" O ASP O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.604A pdb=" N THR O 87 " --> pdb=" O ASP O 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.925A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.544A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.789A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 475 through 481 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.903A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.500A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 649 removed outlier: 3.835A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 removed outlier: 4.240A pdb=" N ILE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.005A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE G 102 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.005A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.423A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'I' and resid 18 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.200A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.821A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.434A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB2, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AB3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AB4, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.261A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.245A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.172A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.275A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.830A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 17 through 20 Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.559A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.559A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.004A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE J 102 " --> pdb=" O THR J 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.004A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 9 through 12 removed outlier: 6.423A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 9 through 12 Processing sheet with id=AD2, first strand: chain 'M' and resid 18 through 24 Processing sheet with id=AD3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.201A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.821A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.434A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AD8, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AD9, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.260A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.245A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 271 through 274 removed outlier: 11.172A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AE4, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.275A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.829A pdb=" N TYR K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 17 through 20 Processing sheet with id=AE8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.558A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.558A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'O' and resid 57 through 59 removed outlier: 5.004A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE O 102 " --> pdb=" O THR O 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 57 through 59 removed outlier: 5.004A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.424A pdb=" N TRP Q 35 " --> pdb=" O MET Q 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 9 through 12 Processing sheet with id=AF7, first strand: chain 'Q' and resid 18 through 24 Processing sheet with id=AF8, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.201A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.821A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.434A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AG3, first strand: chain 'E' and resid 130 through 133 Processing sheet with id=AG4, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AG5, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.261A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.245A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 271 through 274 removed outlier: 11.172A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 305 through 308 Processing sheet with id=AG9, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AH1, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.276A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.829A pdb=" N TYR P 102 " --> pdb=" O ARG P 94 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 17 through 20 Processing sheet with id=AH4, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AH5, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.558A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.558A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) 1047 hydrogen bonds defined for protein. 2673 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: 6.55 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7830 1.34 - 1.46: 6621 1.46 - 1.59: 11124 1.59 - 1.71: 3 1.71 - 1.83: 216 Bond restraints: 25794 Sorted by residual: bond pdb=" C ASN F 618 " pdb=" N LEU F 619 " ideal model delta sigma weight residual 1.335 1.217 0.118 1.30e-02 5.92e+03 8.27e+01 bond pdb=" C ASN B 618 " pdb=" N LEU B 619 " ideal model delta sigma weight residual 1.335 1.217 0.118 1.30e-02 5.92e+03 8.25e+01 bond pdb=" C ASN D 618 " pdb=" N LEU D 619 " ideal model delta sigma weight residual 1.335 1.217 0.118 1.30e-02 5.92e+03 8.21e+01 bond pdb=" C ASN C 392 " pdb=" N SER C 393 " ideal model delta sigma weight residual 1.330 1.241 0.089 1.22e-02 6.72e+03 5.36e+01 bond pdb=" C ASN A 392 " pdb=" N SER A 393 " ideal model delta sigma weight residual 1.330 1.241 0.089 1.22e-02 6.72e+03 5.29e+01 ... (remaining 25789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 33227 1.87 - 3.74: 1327 3.74 - 5.61: 338 5.61 - 7.48: 91 7.48 - 9.35: 18 Bond angle restraints: 35001 Sorted by residual: angle pdb=" C ASN D 618 " pdb=" N LEU D 619 " pdb=" CA LEU D 619 " ideal model delta sigma weight residual 120.38 129.73 -9.35 1.37e+00 5.33e-01 4.66e+01 angle pdb=" C ASN F 618 " pdb=" N LEU F 619 " pdb=" CA LEU F 619 " ideal model delta sigma weight residual 120.38 129.73 -9.35 1.37e+00 5.33e-01 4.66e+01 angle pdb=" C ASN B 618 " pdb=" N LEU B 619 " pdb=" CA LEU B 619 " ideal model delta sigma weight residual 120.38 129.73 -9.35 1.37e+00 5.33e-01 4.65e+01 angle pdb=" CA ASN E 88 " pdb=" CB ASN E 88 " pdb=" CG ASN E 88 " ideal model delta sigma weight residual 112.60 119.06 -6.46 1.00e+00 1.00e+00 4.17e+01 angle pdb=" CA ASN A 88 " pdb=" CB ASN A 88 " pdb=" CG ASN A 88 " ideal model delta sigma weight residual 112.60 119.05 -6.45 1.00e+00 1.00e+00 4.16e+01 ... (remaining 34996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.88: 15225 22.88 - 45.76: 1074 45.76 - 68.63: 204 68.63 - 91.51: 57 91.51 - 114.39: 24 Dihedral angle restraints: 16584 sinusoidal: 7770 harmonic: 8814 Sorted by residual: dihedral pdb=" CB CYS P 98 " pdb=" SG CYS P 98 " pdb=" SG CYS P 100C" pdb=" CB CYS P 100C" ideal model delta sinusoidal sigma weight residual 93.00 162.74 -69.74 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS H 98 " pdb=" SG CYS H 98 " pdb=" SG CYS H 100C" pdb=" CB CYS H 100C" ideal model delta sinusoidal sigma weight residual 93.00 162.73 -69.73 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CB CYS K 98 " pdb=" SG CYS K 98 " pdb=" SG CYS K 100C" pdb=" CB CYS K 100C" ideal model delta sinusoidal sigma weight residual 93.00 162.73 -69.73 1 1.00e+01 1.00e-02 6.27e+01 ... (remaining 16581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 4001 0.129 - 0.258: 134 0.258 - 0.386: 8 0.386 - 0.515: 3 0.515 - 0.644: 3 Chirality restraints: 4149 Sorted by residual: chirality pdb=" C1 NAG g 2 " pdb=" O4 NAG g 1 " pdb=" C2 NAG g 2 " pdb=" O5 NAG g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.19e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.18e+01 chirality pdb=" C1 NAG q 2 " pdb=" O4 NAG q 1 " pdb=" C2 NAG q 2 " pdb=" O5 NAG q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.13e+01 ... (remaining 4146 not shown) Planarity restraints: 4386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 18 " -0.720 9.50e-02 1.11e+02 3.24e-01 7.37e+01 pdb=" NE ARG N 18 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG N 18 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG N 18 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG N 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 18 " 0.720 9.50e-02 1.11e+02 3.24e-01 7.35e+01 pdb=" NE ARG L 18 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG L 18 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG L 18 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG L 18 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 18 " -0.720 9.50e-02 1.11e+02 3.24e-01 7.35e+01 pdb=" NE ARG R 18 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG R 18 " -0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG R 18 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG R 18 " -0.004 2.00e-02 2.50e+03 ... (remaining 4383 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 761 2.69 - 3.24: 22591 3.24 - 3.79: 39448 3.79 - 4.35: 56363 4.35 - 4.90: 91899 Nonbonded interactions: 211062 Sorted by model distance: nonbonded pdb=" OD1 ASP C 113 " pdb=" NH1 ARG C 429 " model vdw 2.136 3.120 nonbonded pdb=" OD1 ASP E 113 " pdb=" NH1 ARG E 429 " model vdw 2.137 3.120 nonbonded pdb=" OD1 ASP A 113 " pdb=" NH1 ARG A 429 " model vdw 2.137 3.120 nonbonded pdb=" O THR Q 26 " pdb=" OD1 ASP Q 27B" model vdw 2.169 3.040 nonbonded pdb=" O THR I 26 " pdb=" OD1 ASP I 27B" model vdw 2.169 3.040 ... (remaining 211057 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'a' selection = chain 'd' selection = chain 'f' selection = chain 'k' selection = chain 'n' selection = chain 'p' selection = chain 'u' } ncs_group { reference = chain 'Y' selection = chain 'i' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.700 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.150 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:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.008 0.537 25938 Z= 0.402 Angle : 1.102 32.586 35385 Z= 0.549 Chirality : 0.057 0.644 4149 Planarity : 0.012 0.324 4341 Dihedral : 16.464 114.391 10800 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.11 % Allowed : 17.35 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.68 (0.15), residues: 3015 helix: -0.43 (0.26), residues: 432 sheet: -0.15 (0.15), residues: 1023 loop : -0.56 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.002 ARG N 18 TYR 0.016 0.002 TYR H 100D PHE 0.020 0.002 PHE E 53 TRP 0.041 0.002 TRP C 427 HIS 0.027 0.002 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00547 (25794) covalent geometry : angle 0.94608 (35001) SS BOND : bond 0.13463 ( 48) SS BOND : angle 8.35945 ( 96) hydrogen bonds : bond 0.12198 ( 924) hydrogen bonds : angle 6.59948 ( 2673) link_ALPHA1-3 : bond 0.00589 ( 6) link_ALPHA1-3 : angle 1.98069 ( 18) link_ALPHA1-6 : bond 0.01882 ( 3) link_ALPHA1-6 : angle 3.71384 ( 9) link_BETA1-4 : bond 0.01424 ( 42) link_BETA1-4 : angle 3.62167 ( 126) link_NAG-ASN : bond 0.02208 ( 45) link_NAG-ASN : angle 4.79534 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 406 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8610 (mmtt) REVERT: B 574 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7840 (mttm) REVERT: H 81 GLU cc_start: 0.8141 (tt0) cc_final: 0.7788 (tt0) REVERT: J 52 ASN cc_start: 0.9085 (p0) cc_final: 0.8817 (p0) REVERT: M 53 GLN cc_start: 0.8522 (mm110) cc_final: 0.8246 (mp10) REVERT: C 166 ARG cc_start: 0.7369 (mtm180) cc_final: 0.6417 (ptt90) REVERT: C 475 MET cc_start: 0.9021 (mmt) cc_final: 0.8728 (mmm) REVERT: D 584 GLU cc_start: 0.8583 (pt0) cc_final: 0.8314 (pt0) REVERT: K 46 GLU cc_start: 0.7982 (tt0) cc_final: 0.7660 (tt0) REVERT: K 69 MET cc_start: 0.8796 (mtt) cc_final: 0.8540 (mtm) REVERT: K 81 GLU cc_start: 0.8179 (tt0) cc_final: 0.7811 (tt0) REVERT: Q 79 GLN cc_start: 0.7427 (mt0) cc_final: 0.6968 (mt0) REVERT: E 475 MET cc_start: 0.8984 (mmt) cc_final: 0.8779 (mpp) REVERT: F 577 GLN cc_start: 0.8220 (mt0) cc_final: 0.8005 (mt0) REVERT: P 54 ARG cc_start: 0.8817 (mmt90) cc_final: 0.8568 (tpt170) REVERT: P 81 GLU cc_start: 0.8119 (tt0) cc_final: 0.7721 (tt0) outliers start: 3 outliers final: 0 residues processed: 406 average time/residue: 0.6857 time to fit residues: 320.4196 Evaluate side-chains 348 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 76 ASN G 82AHIS I 38 GLN A 130 GLN A 173 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN B 658 GLN H 61 GLN J 3 GLN J 76 ASN M 38 GLN C 130 GLN C 173 HIS C 355 ASN C 377 ASN C 428 GLN D 650 GLN O 3 GLN O 76 ASN O 82AHIS O 100BGLN Q 38 GLN Q 69 ASN E 130 GLN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.173305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137061 restraints weight = 26877.029| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.90 r_work: 0.3308 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25938 Z= 0.218 Angle : 0.725 8.753 35385 Z= 0.357 Chirality : 0.047 0.211 4149 Planarity : 0.005 0.034 4341 Dihedral : 9.719 105.452 5289 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.76 % Allowed : 17.16 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.51 (0.15), residues: 3015 helix: -0.20 (0.26), residues: 435 sheet: -0.06 (0.16), residues: 969 loop : -0.46 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 542 TYR 0.013 0.002 TYR M 49 PHE 0.015 0.002 PHE G 100H TRP 0.026 0.002 TRP C 427 HIS 0.004 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00507 (25794) covalent geometry : angle 0.68336 (35001) SS BOND : bond 0.00390 ( 48) SS BOND : angle 1.52161 ( 96) hydrogen bonds : bond 0.04645 ( 924) hydrogen bonds : angle 5.63367 ( 2673) link_ALPHA1-3 : bond 0.00595 ( 6) link_ALPHA1-3 : angle 2.82831 ( 18) link_ALPHA1-6 : bond 0.01545 ( 3) link_ALPHA1-6 : angle 2.85995 ( 9) link_BETA1-4 : bond 0.00652 ( 42) link_BETA1-4 : angle 2.47033 ( 126) link_NAG-ASN : bond 0.00864 ( 45) link_NAG-ASN : angle 2.76689 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 362 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7333 (mmm160) REVERT: A 84 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8807 (mp) REVERT: A 439 ILE cc_start: 0.9072 (mm) cc_final: 0.8860 (mm) REVERT: B 574 LYS cc_start: 0.8481 (mmtp) cc_final: 0.8171 (mttm) REVERT: H 54 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8859 (tpt170) REVERT: H 81 GLU cc_start: 0.8250 (tt0) cc_final: 0.7792 (tt0) REVERT: M 95 GLN cc_start: 0.8587 (mp-120) cc_final: 0.8234 (mm110) REVERT: C 61 TYR cc_start: 0.5156 (OUTLIER) cc_final: 0.4210 (t80) REVERT: C 84 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8740 (mp) REVERT: D 584 GLU cc_start: 0.8808 (pt0) cc_final: 0.8457 (pt0) REVERT: K 46 GLU cc_start: 0.8179 (tt0) cc_final: 0.7889 (tt0) REVERT: K 81 GLU cc_start: 0.8224 (tt0) cc_final: 0.7786 (tt0) REVERT: O 23 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6540 (mmm160) REVERT: Q 31 ASN cc_start: 0.8727 (m-40) cc_final: 0.8507 (m-40) REVERT: E 61 TYR cc_start: 0.5188 (OUTLIER) cc_final: 0.4974 (m-10) REVERT: E 121 LYS cc_start: 0.9162 (mtmt) cc_final: 0.8848 (mttm) REVERT: E 475 MET cc_start: 0.8945 (mmt) cc_final: 0.8557 (mpm) REVERT: F 577 GLN cc_start: 0.8454 (mt0) cc_final: 0.8217 (mt0) REVERT: P 54 ARG cc_start: 0.9094 (mmt90) cc_final: 0.8865 (tpt170) outliers start: 73 outliers final: 27 residues processed: 410 average time/residue: 0.6301 time to fit residues: 299.7020 Evaluate side-chains 378 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 344 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain R residue 1 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 195 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 183 optimal weight: 0.3980 chunk 186 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 262 optimal weight: 0.0980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 114 GLN C 173 HIS D 653 GLN O 3 GLN O 100BGLN Q 69 ASN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.173931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.137767 restraints weight = 26784.770| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.17 r_work: 0.3306 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25938 Z= 0.151 Angle : 0.634 9.090 35385 Z= 0.312 Chirality : 0.045 0.202 4149 Planarity : 0.004 0.035 4341 Dihedral : 8.438 103.421 5289 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.76 % Allowed : 17.65 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.34 (0.15), residues: 3015 helix: 0.03 (0.26), residues: 432 sheet: 0.07 (0.16), residues: 987 loop : -0.39 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 169 TYR 0.011 0.001 TYR Q 96 PHE 0.012 0.001 PHE A 383 TRP 0.017 0.002 TRP H 50 HIS 0.003 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00342 (25794) covalent geometry : angle 0.59586 (35001) SS BOND : bond 0.00291 ( 48) SS BOND : angle 1.31738 ( 96) hydrogen bonds : bond 0.04018 ( 924) hydrogen bonds : angle 5.40714 ( 2673) link_ALPHA1-3 : bond 0.00743 ( 6) link_ALPHA1-3 : angle 2.82358 ( 18) link_ALPHA1-6 : bond 0.02406 ( 3) link_ALPHA1-6 : angle 3.14069 ( 9) link_BETA1-4 : bond 0.00575 ( 42) link_BETA1-4 : angle 2.14578 ( 126) link_NAG-ASN : bond 0.00647 ( 45) link_NAG-ASN : angle 2.47708 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 366 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7239 (mmm160) REVERT: A 84 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8690 (mp) REVERT: A 121 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8859 (mttt) REVERT: A 429 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6630 (mpp80) REVERT: A 439 ILE cc_start: 0.9030 (mm) cc_final: 0.8804 (mm) REVERT: B 574 LYS cc_start: 0.8423 (mmtp) cc_final: 0.8113 (mttm) REVERT: H 54 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8844 (tpt170) REVERT: M 53 GLN cc_start: 0.8604 (mm110) cc_final: 0.8219 (mm110) REVERT: C 61 TYR cc_start: 0.5131 (OUTLIER) cc_final: 0.4298 (t80) REVERT: C 84 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8635 (mp) REVERT: C 479 TRP cc_start: 0.7604 (m-10) cc_final: 0.7303 (m-10) REVERT: D 584 GLU cc_start: 0.8697 (pt0) cc_final: 0.8468 (pt0) REVERT: D 647 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7222 (tm-30) REVERT: K 46 GLU cc_start: 0.8175 (tt0) cc_final: 0.7872 (tt0) REVERT: K 69 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7899 (mtm) REVERT: K 81 GLU cc_start: 0.8273 (tt0) cc_final: 0.7826 (tt0) REVERT: N 4 MET cc_start: 0.7625 (mtp) cc_final: 0.7385 (mtp) REVERT: N 33 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8187 (tt) REVERT: O 23 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6643 (mmm160) REVERT: E 61 TYR cc_start: 0.5118 (OUTLIER) cc_final: 0.4369 (t80) REVERT: E 121 LYS cc_start: 0.9189 (mtmt) cc_final: 0.8870 (mttm) REVERT: E 475 MET cc_start: 0.8898 (mmt) cc_final: 0.8501 (mpm) REVERT: F 577 GLN cc_start: 0.8474 (mt0) cc_final: 0.8236 (mt0) REVERT: F 659 ASP cc_start: 0.8811 (t70) cc_final: 0.8558 (t70) REVERT: P 54 ARG cc_start: 0.9067 (mmt90) cc_final: 0.8859 (tpt170) REVERT: P 83 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.6161 (ptp-170) outliers start: 73 outliers final: 22 residues processed: 414 average time/residue: 0.5809 time to fit residues: 279.3841 Evaluate side-chains 372 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 339 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 83 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 100 optimal weight: 7.9990 chunk 82 optimal weight: 0.3980 chunk 283 optimal weight: 0.0970 chunk 241 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 GLN A 82 GLN A 114 GLN J 3 GLN J 105 GLN C 428 GLN D 653 GLN O 3 GLN O 100BGLN Q 69 ASN E 173 HIS E 355 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.174884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.140858 restraints weight = 26726.958| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.03 r_work: 0.3359 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25938 Z= 0.121 Angle : 0.592 9.077 35385 Z= 0.290 Chirality : 0.043 0.252 4149 Planarity : 0.004 0.040 4341 Dihedral : 7.825 101.331 5289 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.61 % Allowed : 17.99 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.18 (0.15), residues: 3015 helix: 0.22 (0.26), residues: 432 sheet: 0.17 (0.15), residues: 987 loop : -0.30 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 169 TYR 0.014 0.001 TYR J 91 PHE 0.012 0.001 PHE A 383 TRP 0.018 0.001 TRP H 50 HIS 0.003 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00266 (25794) covalent geometry : angle 0.55247 (35001) SS BOND : bond 0.00252 ( 48) SS BOND : angle 1.33404 ( 96) hydrogen bonds : bond 0.03638 ( 924) hydrogen bonds : angle 5.24159 ( 2673) link_ALPHA1-3 : bond 0.00831 ( 6) link_ALPHA1-3 : angle 2.85138 ( 18) link_ALPHA1-6 : bond 0.02711 ( 3) link_ALPHA1-6 : angle 3.41916 ( 9) link_BETA1-4 : bond 0.00565 ( 42) link_BETA1-4 : angle 1.91721 ( 126) link_NAG-ASN : bond 0.00567 ( 45) link_NAG-ASN : angle 2.50041 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 370 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7340 (mmm160) REVERT: A 121 LYS cc_start: 0.9253 (mtpt) cc_final: 0.8841 (mttt) REVERT: A 429 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6304 (mtm180) REVERT: B 574 LYS cc_start: 0.8405 (mmtp) cc_final: 0.8113 (mttm) REVERT: H 54 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8818 (tpt170) REVERT: H 69 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7879 (mtt) REVERT: H 81 GLU cc_start: 0.8048 (tt0) cc_final: 0.7511 (tt0) REVERT: H 108 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7819 (tt) REVERT: L 33 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8128 (tt) REVERT: M 53 GLN cc_start: 0.8561 (mm110) cc_final: 0.8106 (mm110) REVERT: M 95 GLN cc_start: 0.8545 (mp-120) cc_final: 0.8140 (mm110) REVERT: C 61 TYR cc_start: 0.5142 (OUTLIER) cc_final: 0.4325 (t80) REVERT: C 479 TRP cc_start: 0.7572 (m-10) cc_final: 0.7252 (m-10) REVERT: D 577 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: D 647 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6959 (tm-30) REVERT: K 46 GLU cc_start: 0.8157 (tt0) cc_final: 0.7853 (tt0) REVERT: K 81 GLU cc_start: 0.8225 (tt0) cc_final: 0.7749 (tt0) REVERT: N 33 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8148 (tt) REVERT: E 61 TYR cc_start: 0.5169 (OUTLIER) cc_final: 0.4418 (t80) REVERT: E 121 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8828 (mttm) REVERT: E 444 ARG cc_start: 0.8233 (ttt-90) cc_final: 0.8018 (ttt-90) REVERT: E 475 MET cc_start: 0.8927 (mmt) cc_final: 0.8337 (mpm) REVERT: F 577 GLN cc_start: 0.8462 (mt0) cc_final: 0.8244 (mt0) REVERT: P 69 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8537 (mpt) REVERT: P 100 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8229 (p0) REVERT: R 33 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8089 (tt) outliers start: 69 outliers final: 31 residues processed: 413 average time/residue: 0.6393 time to fit residues: 305.9727 Evaluate side-chains 388 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 344 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 69 MET Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 154 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 252 optimal weight: 0.7980 chunk 198 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 GLN A 82 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN J 105 GLN C 173 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 100BGLN Q 69 ASN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.172098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136315 restraints weight = 26685.579| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.88 r_work: 0.3260 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25938 Z= 0.190 Angle : 0.656 8.934 35385 Z= 0.322 Chirality : 0.045 0.260 4149 Planarity : 0.004 0.043 4341 Dihedral : 7.775 97.796 5289 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.14 % Allowed : 18.07 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.19 (0.15), residues: 3015 helix: 0.22 (0.26), residues: 432 sheet: 0.22 (0.16), residues: 993 loop : -0.36 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 169 TYR 0.018 0.002 TYR J 91 PHE 0.014 0.002 PHE A 383 TRP 0.021 0.002 TRP H 50 HIS 0.003 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00442 (25794) covalent geometry : angle 0.61608 (35001) SS BOND : bond 0.00330 ( 48) SS BOND : angle 1.50996 ( 96) hydrogen bonds : bond 0.04169 ( 924) hydrogen bonds : angle 5.28596 ( 2673) link_ALPHA1-3 : bond 0.00837 ( 6) link_ALPHA1-3 : angle 2.99692 ( 18) link_ALPHA1-6 : bond 0.02754 ( 3) link_ALPHA1-6 : angle 3.53573 ( 9) link_BETA1-4 : bond 0.00542 ( 42) link_BETA1-4 : angle 1.89072 ( 126) link_NAG-ASN : bond 0.00699 ( 45) link_NAG-ASN : angle 2.70736 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 356 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7255 (mmm160) REVERT: A 84 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8776 (mp) REVERT: A 121 LYS cc_start: 0.9300 (mtpt) cc_final: 0.8890 (mttt) REVERT: A 129 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8989 (mt) REVERT: A 267 GLU cc_start: 0.7434 (mp0) cc_final: 0.7213 (mp0) REVERT: A 429 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6357 (mtm180) REVERT: B 574 LYS cc_start: 0.8442 (mmtp) cc_final: 0.8174 (mttm) REVERT: H 21 SER cc_start: 0.8636 (p) cc_final: 0.8264 (t) REVERT: H 54 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8849 (tpt170) REVERT: H 81 GLU cc_start: 0.8185 (tt0) cc_final: 0.7820 (tt0) REVERT: H 108 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7882 (tt) REVERT: C 61 TYR cc_start: 0.5163 (OUTLIER) cc_final: 0.4317 (t80) REVERT: C 84 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8716 (mp) REVERT: C 479 TRP cc_start: 0.7676 (m-10) cc_final: 0.7103 (m-10) REVERT: D 577 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8249 (mt0) REVERT: D 647 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7660 (tm-30) REVERT: D 650 GLN cc_start: 0.6838 (mm-40) cc_final: 0.6608 (tt0) REVERT: K 46 GLU cc_start: 0.8286 (tt0) cc_final: 0.7993 (tt0) REVERT: K 81 GLU cc_start: 0.8249 (tt0) cc_final: 0.7856 (tt0) REVERT: N 33 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8212 (tt) REVERT: O 23 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6662 (mmm160) REVERT: E 61 TYR cc_start: 0.5139 (OUTLIER) cc_final: 0.4339 (t80) REVERT: E 84 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8668 (mp) REVERT: E 121 LYS cc_start: 0.9203 (mtmt) cc_final: 0.8930 (mttm) REVERT: E 327 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6847 (mtm180) REVERT: E 475 MET cc_start: 0.8948 (mmt) cc_final: 0.8582 (mpm) REVERT: F 577 GLN cc_start: 0.8454 (mt0) cc_final: 0.8223 (mt0) REVERT: F 647 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: P 83 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6247 (ptt180) REVERT: P 100 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8500 (p0) REVERT: R 33 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8148 (tt) outliers start: 83 outliers final: 38 residues processed: 409 average time/residue: 0.6296 time to fit residues: 298.8116 Evaluate side-chains 396 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 340 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 133 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 82 optimal weight: 0.0970 chunk 155 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 GLN A 82 GLN J 105 GLN C 428 GLN D 653 GLN O 3 GLN O 100BGLN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.173810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138124 restraints weight = 26831.126| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.89 r_work: 0.3286 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25938 Z= 0.146 Angle : 0.606 9.107 35385 Z= 0.298 Chirality : 0.044 0.257 4149 Planarity : 0.004 0.031 4341 Dihedral : 7.553 95.060 5289 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.91 % Allowed : 18.48 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.08 (0.15), residues: 3015 helix: 0.36 (0.26), residues: 432 sheet: 0.28 (0.15), residues: 993 loop : -0.30 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 169 TYR 0.016 0.001 TYR J 91 PHE 0.012 0.001 PHE A 383 TRP 0.022 0.002 TRP H 50 HIS 0.003 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00331 (25794) covalent geometry : angle 0.56594 (35001) SS BOND : bond 0.00259 ( 48) SS BOND : angle 1.32849 ( 96) hydrogen bonds : bond 0.03817 ( 924) hydrogen bonds : angle 5.21701 ( 2673) link_ALPHA1-3 : bond 0.00876 ( 6) link_ALPHA1-3 : angle 3.04565 ( 18) link_ALPHA1-6 : bond 0.02905 ( 3) link_ALPHA1-6 : angle 3.64144 ( 9) link_BETA1-4 : bond 0.00525 ( 42) link_BETA1-4 : angle 1.76138 ( 126) link_NAG-ASN : bond 0.00596 ( 45) link_NAG-ASN : angle 2.66366 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 360 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7338 (mmm160) REVERT: A 84 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8691 (mp) REVERT: A 103 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8485 (tm-30) REVERT: A 114 GLN cc_start: 0.7952 (tp40) cc_final: 0.7742 (tp-100) REVERT: A 121 LYS cc_start: 0.9296 (mtpt) cc_final: 0.8879 (mttt) REVERT: A 315 GLN cc_start: 0.7935 (mt0) cc_final: 0.7389 (mm110) REVERT: A 429 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6403 (mtm180) REVERT: B 574 LYS cc_start: 0.8417 (mmtp) cc_final: 0.8142 (mttm) REVERT: H 21 SER cc_start: 0.8613 (p) cc_final: 0.8264 (t) REVERT: H 54 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8877 (tpt170) REVERT: H 108 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7905 (tt) REVERT: M 95 GLN cc_start: 0.8546 (mp-120) cc_final: 0.8141 (mm110) REVERT: C 61 TYR cc_start: 0.5180 (OUTLIER) cc_final: 0.4347 (t80) REVERT: C 84 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8599 (mp) REVERT: C 103 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: C 479 TRP cc_start: 0.7633 (m-10) cc_final: 0.7124 (m-10) REVERT: D 577 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8228 (mt0) REVERT: D 647 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7542 (tm-30) REVERT: D 650 GLN cc_start: 0.6924 (mm-40) cc_final: 0.6657 (tt0) REVERT: K 46 GLU cc_start: 0.8221 (tt0) cc_final: 0.7918 (tt0) REVERT: N 33 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8241 (tt) REVERT: O 23 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6684 (mmm160) REVERT: E 61 TYR cc_start: 0.5260 (OUTLIER) cc_final: 0.4487 (t80) REVERT: E 84 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8623 (mp) REVERT: E 121 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8925 (mttm) REVERT: E 315 GLN cc_start: 0.8055 (mt0) cc_final: 0.7595 (mm110) REVERT: E 327 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6819 (mtm180) REVERT: E 475 MET cc_start: 0.8952 (mmt) cc_final: 0.8421 (mpm) REVERT: F 536 THR cc_start: 0.8955 (p) cc_final: 0.8615 (p) REVERT: F 577 GLN cc_start: 0.8470 (mt0) cc_final: 0.8248 (mt0) REVERT: F 585 ARG cc_start: 0.8694 (mtp180) cc_final: 0.8446 (mtp-110) REVERT: P 83 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.6246 (ptt180) REVERT: P 100 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8381 (p0) outliers start: 77 outliers final: 35 residues processed: 413 average time/residue: 0.6651 time to fit residues: 317.5764 Evaluate side-chains 397 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 345 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 100 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 245 optimal weight: 3.9990 chunk 257 optimal weight: 0.2980 chunk 9 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN M 69 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 653 GLN O 3 GLN O 100BGLN Q 69 ASN Q 95 GLN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.172286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.136467 restraints weight = 26636.801| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.86 r_work: 0.3265 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25938 Z= 0.187 Angle : 0.647 9.005 35385 Z= 0.319 Chirality : 0.045 0.238 4149 Planarity : 0.004 0.034 4341 Dihedral : 7.528 90.733 5289 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 3.21 % Allowed : 18.48 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.13 (0.15), residues: 3015 helix: 0.35 (0.26), residues: 432 sheet: 0.30 (0.16), residues: 957 loop : -0.37 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 542 TYR 0.017 0.001 TYR J 91 PHE 0.014 0.002 PHE A 383 TRP 0.021 0.002 TRP P 50 HIS 0.003 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00434 (25794) covalent geometry : angle 0.60949 (35001) SS BOND : bond 0.00330 ( 48) SS BOND : angle 1.38168 ( 96) hydrogen bonds : bond 0.04145 ( 924) hydrogen bonds : angle 5.25042 ( 2673) link_ALPHA1-3 : bond 0.00865 ( 6) link_ALPHA1-3 : angle 3.19470 ( 18) link_ALPHA1-6 : bond 0.02827 ( 3) link_ALPHA1-6 : angle 3.64773 ( 9) link_BETA1-4 : bond 0.00522 ( 42) link_BETA1-4 : angle 1.71354 ( 126) link_NAG-ASN : bond 0.00644 ( 45) link_NAG-ASN : angle 2.68581 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 353 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7297 (mmm160) REVERT: A 84 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8766 (mp) REVERT: A 103 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8483 (tm-30) REVERT: A 114 GLN cc_start: 0.8002 (tp40) cc_final: 0.7777 (tp-100) REVERT: A 121 LYS cc_start: 0.9306 (mtpt) cc_final: 0.8886 (mttt) REVERT: A 315 GLN cc_start: 0.7973 (mt0) cc_final: 0.7460 (mm110) REVERT: A 429 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6449 (mtm180) REVERT: B 574 LYS cc_start: 0.8429 (mmtp) cc_final: 0.8164 (mttm) REVERT: H 21 SER cc_start: 0.8664 (p) cc_final: 0.8310 (t) REVERT: H 54 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8849 (tpt170) REVERT: L 33 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8176 (tt) REVERT: C 61 TYR cc_start: 0.5153 (OUTLIER) cc_final: 0.4300 (t80) REVERT: C 84 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8677 (mp) REVERT: C 103 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: C 479 TRP cc_start: 0.7690 (m-10) cc_final: 0.7095 (m-10) REVERT: D 574 LYS cc_start: 0.8345 (mmtp) cc_final: 0.8038 (mttp) REVERT: D 577 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8239 (mt0) REVERT: D 650 GLN cc_start: 0.7271 (mm-40) cc_final: 0.6990 (tt0) REVERT: K 21 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8324 (m) REVERT: K 46 GLU cc_start: 0.8254 (tt0) cc_final: 0.7958 (tt0) REVERT: N 33 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8273 (tt) REVERT: O 23 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6667 (mmm160) REVERT: E 61 TYR cc_start: 0.5308 (OUTLIER) cc_final: 0.4442 (t80) REVERT: E 84 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8650 (mp) REVERT: E 121 LYS cc_start: 0.9213 (mtmt) cc_final: 0.8944 (mttm) REVERT: E 315 GLN cc_start: 0.8083 (mt0) cc_final: 0.7617 (mm110) REVERT: E 322 ASP cc_start: 0.7794 (t0) cc_final: 0.7564 (m-30) REVERT: E 327 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6855 (mtm180) REVERT: E 475 MET cc_start: 0.8950 (mmt) cc_final: 0.8472 (mpm) REVERT: F 577 GLN cc_start: 0.8443 (mt0) cc_final: 0.8237 (mt0) REVERT: P 83 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.6267 (ptt180) REVERT: P 100 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8521 (p0) outliers start: 85 outliers final: 39 residues processed: 410 average time/residue: 0.6565 time to fit residues: 311.9593 Evaluate side-chains 401 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 344 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 100 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 49 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 254 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 179 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 GLN A 82 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN J 105 GLN M 69 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 100BGLN Q 95 GLN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.172374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.136390 restraints weight = 26700.719| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.89 r_work: 0.3272 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25938 Z= 0.165 Angle : 0.629 8.759 35385 Z= 0.309 Chirality : 0.044 0.265 4149 Planarity : 0.004 0.035 4341 Dihedral : 7.445 88.678 5289 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.75 % Favored : 97.21 % Rotamer: Outliers : 2.87 % Allowed : 18.82 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.09 (0.15), residues: 3015 helix: 0.39 (0.26), residues: 432 sheet: 0.36 (0.16), residues: 951 loop : -0.37 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 542 TYR 0.016 0.001 TYR J 91 PHE 0.012 0.001 PHE A 383 TRP 0.021 0.002 TRP H 50 HIS 0.003 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00379 (25794) covalent geometry : angle 0.59031 (35001) SS BOND : bond 0.00289 ( 48) SS BOND : angle 1.31623 ( 96) hydrogen bonds : bond 0.03970 ( 924) hydrogen bonds : angle 5.22757 ( 2673) link_ALPHA1-3 : bond 0.00888 ( 6) link_ALPHA1-3 : angle 3.23770 ( 18) link_ALPHA1-6 : bond 0.02850 ( 3) link_ALPHA1-6 : angle 3.65663 ( 9) link_BETA1-4 : bond 0.00526 ( 42) link_BETA1-4 : angle 1.69412 ( 126) link_NAG-ASN : bond 0.00681 ( 45) link_NAG-ASN : angle 2.66152 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 348 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7297 (mmm160) REVERT: I 31 ASN cc_start: 0.8730 (m110) cc_final: 0.8407 (m-40) REVERT: A 84 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8711 (mp) REVERT: A 103 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: A 121 LYS cc_start: 0.9298 (mtpt) cc_final: 0.8892 (mttt) REVERT: A 315 GLN cc_start: 0.7961 (mt0) cc_final: 0.7449 (mm110) REVERT: A 429 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6379 (mtm180) REVERT: B 574 LYS cc_start: 0.8410 (mmtp) cc_final: 0.8146 (mttm) REVERT: H 21 SER cc_start: 0.8652 (p) cc_final: 0.8307 (t) REVERT: H 54 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8848 (tpt170) REVERT: L 33 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8169 (tt) REVERT: C 61 TYR cc_start: 0.5134 (OUTLIER) cc_final: 0.4269 (t80) REVERT: C 84 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8627 (mp) REVERT: C 103 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: C 327 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6917 (mtm180) REVERT: C 479 TRP cc_start: 0.7671 (m-10) cc_final: 0.7086 (m-10) REVERT: D 577 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8223 (mt0) REVERT: D 650 GLN cc_start: 0.7319 (mm-40) cc_final: 0.7001 (tt0) REVERT: K 21 SER cc_start: 0.8624 (p) cc_final: 0.8333 (m) REVERT: K 46 GLU cc_start: 0.8278 (tt0) cc_final: 0.7989 (tt0) REVERT: O 23 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6648 (mmm160) REVERT: E 61 TYR cc_start: 0.5346 (OUTLIER) cc_final: 0.4455 (t80) REVERT: E 84 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8630 (mp) REVERT: E 121 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8934 (mttm) REVERT: E 315 GLN cc_start: 0.8058 (mt0) cc_final: 0.7592 (mm110) REVERT: E 322 ASP cc_start: 0.7778 (t0) cc_final: 0.7559 (m-30) REVERT: E 327 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6848 (mtm180) REVERT: E 475 MET cc_start: 0.8947 (mmt) cc_final: 0.8470 (mpm) REVERT: E 479 TRP cc_start: 0.7798 (m-10) cc_final: 0.7375 (m-10) REVERT: F 577 GLN cc_start: 0.8434 (mt0) cc_final: 0.8206 (mt0) REVERT: P 83 ARG cc_start: 0.6498 (OUTLIER) cc_final: 0.6251 (ptt180) REVERT: P 100 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8522 (p0) outliers start: 76 outliers final: 42 residues processed: 397 average time/residue: 0.6466 time to fit residues: 297.4714 Evaluate side-chains 399 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 340 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 100 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 258 optimal weight: 0.0770 chunk 256 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 289 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 GLN A 82 GLN A 114 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN O 3 GLN O 100BGLN Q 69 ASN Q 95 GLN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.172317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.136891 restraints weight = 26753.101| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.87 r_work: 0.3244 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25938 Z= 0.185 Angle : 0.645 8.805 35385 Z= 0.318 Chirality : 0.045 0.270 4149 Planarity : 0.004 0.033 4341 Dihedral : 7.406 85.606 5289 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 2.80 % Allowed : 19.12 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.13 (0.15), residues: 3015 helix: 0.37 (0.26), residues: 432 sheet: 0.33 (0.16), residues: 957 loop : -0.39 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 169 TYR 0.016 0.001 TYR J 91 PHE 0.013 0.002 PHE A 383 TRP 0.021 0.002 TRP H 50 HIS 0.004 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00430 (25794) covalent geometry : angle 0.60782 (35001) SS BOND : bond 0.00309 ( 48) SS BOND : angle 1.35695 ( 96) hydrogen bonds : bond 0.04100 ( 924) hydrogen bonds : angle 5.23586 ( 2673) link_ALPHA1-3 : bond 0.00892 ( 6) link_ALPHA1-3 : angle 3.32269 ( 18) link_ALPHA1-6 : bond 0.02871 ( 3) link_ALPHA1-6 : angle 3.70159 ( 9) link_BETA1-4 : bond 0.00519 ( 42) link_BETA1-4 : angle 1.65408 ( 126) link_NAG-ASN : bond 0.00688 ( 45) link_NAG-ASN : angle 2.67924 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 351 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7230 (mmm160) REVERT: I 31 ASN cc_start: 0.8770 (m110) cc_final: 0.8465 (m-40) REVERT: A 84 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8776 (mp) REVERT: A 103 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8509 (tm-30) REVERT: A 121 LYS cc_start: 0.9317 (mtpt) cc_final: 0.8907 (mttt) REVERT: A 315 GLN cc_start: 0.8024 (mt0) cc_final: 0.7492 (mm110) REVERT: A 429 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6395 (mtm180) REVERT: B 574 LYS cc_start: 0.8492 (mmtp) cc_final: 0.8238 (mttm) REVERT: H 21 SER cc_start: 0.8626 (p) cc_final: 0.8285 (t) REVERT: H 54 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8858 (tpt170) REVERT: L 33 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8187 (tt) REVERT: C 61 TYR cc_start: 0.5095 (OUTLIER) cc_final: 0.4213 (t80) REVERT: C 84 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8699 (mp) REVERT: C 103 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: C 129 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9008 (mt) REVERT: C 327 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.6892 (mtm180) REVERT: C 479 TRP cc_start: 0.7704 (m-10) cc_final: 0.7099 (m-10) REVERT: D 574 LYS cc_start: 0.8361 (mmtp) cc_final: 0.8126 (mttm) REVERT: D 577 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: D 650 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7094 (tt0) REVERT: K 21 SER cc_start: 0.8672 (p) cc_final: 0.8345 (m) REVERT: K 46 GLU cc_start: 0.8299 (tt0) cc_final: 0.8002 (tt0) REVERT: O 23 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6679 (mmm160) REVERT: E 61 TYR cc_start: 0.5425 (OUTLIER) cc_final: 0.4438 (t80) REVERT: E 84 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8678 (mp) REVERT: E 121 LYS cc_start: 0.9245 (mtmt) cc_final: 0.8957 (mttm) REVERT: E 315 GLN cc_start: 0.8105 (mt0) cc_final: 0.7681 (mm110) REVERT: E 322 ASP cc_start: 0.7814 (t0) cc_final: 0.7581 (m-30) REVERT: E 327 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.6818 (mtm180) REVERT: E 475 MET cc_start: 0.8979 (mmt) cc_final: 0.8511 (mpm) REVERT: E 479 TRP cc_start: 0.7830 (m-10) cc_final: 0.7362 (m-10) REVERT: F 577 GLN cc_start: 0.8457 (mt0) cc_final: 0.8221 (mt0) REVERT: P 83 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.6244 (ptt180) REVERT: P 100 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8591 (p0) REVERT: R 33 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8168 (tt) outliers start: 74 outliers final: 42 residues processed: 400 average time/residue: 0.6371 time to fit residues: 295.5892 Evaluate side-chains 408 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 347 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 153 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 293 optimal weight: 6.9990 chunk 240 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN M 69 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 100BGLN Q 95 GLN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.171820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.135733 restraints weight = 26642.311| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.88 r_work: 0.3256 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 25938 Z= 0.200 Angle : 0.662 8.854 35385 Z= 0.326 Chirality : 0.045 0.254 4149 Planarity : 0.004 0.033 4341 Dihedral : 7.388 82.594 5289 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.79 % Favored : 97.11 % Rotamer: Outliers : 2.53 % Allowed : 19.46 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.16 (0.15), residues: 3015 helix: 0.30 (0.26), residues: 432 sheet: 0.31 (0.16), residues: 957 loop : -0.41 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 169 TYR 0.016 0.002 TYR J 91 PHE 0.014 0.002 PHE A 383 TRP 0.020 0.002 TRP H 50 HIS 0.004 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00469 (25794) covalent geometry : angle 0.62402 (35001) SS BOND : bond 0.00332 ( 48) SS BOND : angle 1.41151 ( 96) hydrogen bonds : bond 0.04208 ( 924) hydrogen bonds : angle 5.25042 ( 2673) link_ALPHA1-3 : bond 0.00889 ( 6) link_ALPHA1-3 : angle 3.40070 ( 18) link_ALPHA1-6 : bond 0.02849 ( 3) link_ALPHA1-6 : angle 3.70909 ( 9) link_BETA1-4 : bond 0.00519 ( 42) link_BETA1-4 : angle 1.65189 ( 126) link_NAG-ASN : bond 0.00691 ( 45) link_NAG-ASN : angle 2.70533 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 347 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7193 (mmm160) REVERT: I 31 ASN cc_start: 0.8761 (m110) cc_final: 0.8439 (m-40) REVERT: A 84 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 103 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8483 (tm-30) REVERT: A 121 LYS cc_start: 0.9314 (mtpt) cc_final: 0.8903 (mttt) REVERT: A 315 GLN cc_start: 0.7978 (mt0) cc_final: 0.7461 (mm110) REVERT: A 429 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6281 (mtm180) REVERT: B 574 LYS cc_start: 0.8508 (mmtp) cc_final: 0.8249 (mttm) REVERT: H 21 SER cc_start: 0.8625 (p) cc_final: 0.8295 (t) REVERT: H 54 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8853 (tpt170) REVERT: L 33 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8193 (tt) REVERT: C 61 TYR cc_start: 0.5128 (OUTLIER) cc_final: 0.4222 (t80) REVERT: C 103 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: C 129 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8993 (mt) REVERT: C 327 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6903 (mtm180) REVERT: C 479 TRP cc_start: 0.7689 (m-10) cc_final: 0.7069 (m-10) REVERT: D 574 LYS cc_start: 0.8343 (mmtp) cc_final: 0.8036 (mttp) REVERT: D 577 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8231 (mt0) REVERT: K 21 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8328 (m) REVERT: K 46 GLU cc_start: 0.8265 (tt0) cc_final: 0.7989 (tt0) REVERT: O 23 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6661 (mmm160) REVERT: E 61 TYR cc_start: 0.5470 (OUTLIER) cc_final: 0.4415 (t80) REVERT: E 84 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8668 (mp) REVERT: E 121 LYS cc_start: 0.9248 (mtmt) cc_final: 0.8959 (mttm) REVERT: E 315 GLN cc_start: 0.8083 (mt0) cc_final: 0.7665 (mm110) REVERT: E 322 ASP cc_start: 0.7797 (t0) cc_final: 0.7568 (m-30) REVERT: E 327 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6821 (mtm180) REVERT: E 475 MET cc_start: 0.8960 (mmt) cc_final: 0.8507 (mpm) REVERT: E 479 TRP cc_start: 0.7793 (m-10) cc_final: 0.7339 (m-10) REVERT: F 577 GLN cc_start: 0.8441 (mt0) cc_final: 0.8206 (mt0) REVERT: P 83 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.6238 (ptt180) REVERT: R 33 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8176 (tt) outliers start: 67 outliers final: 42 residues processed: 391 average time/residue: 0.6494 time to fit residues: 294.7873 Evaluate side-chains 403 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 343 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 429 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain N residue 1 ASN Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 100 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 83 ARG Chi-restraints excluded: chain R residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 263 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 298 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 chunk 3 optimal weight: 5.9990 chunk 280 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 GLN A 82 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN M 69 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 100BGLN Q 69 ASN Q 95 GLN E 173 HIS E 355 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.171079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135550 restraints weight = 26746.146| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.88 r_work: 0.3232 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25938 Z= 0.217 Angle : 0.682 9.047 35385 Z= 0.335 Chirality : 0.046 0.253 4149 Planarity : 0.004 0.034 4341 Dihedral : 7.372 78.839 5289 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Rotamer: Outliers : 2.53 % Allowed : 19.43 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 (0.15), residues: 3015 helix: 0.26 (0.26), residues: 432 sheet: 0.29 (0.16), residues: 957 loop : -0.43 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 169 TYR 0.023 0.002 TYR K 91 PHE 0.015 0.002 PHE C 353 TRP 0.020 0.002 TRP H 50 HIS 0.004 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00512 (25794) covalent geometry : angle 0.64413 (35001) SS BOND : bond 0.00360 ( 48) SS BOND : angle 1.46804 ( 96) hydrogen bonds : bond 0.04339 ( 924) hydrogen bonds : angle 5.27492 ( 2673) link_ALPHA1-3 : bond 0.00848 ( 6) link_ALPHA1-3 : angle 3.48524 ( 18) link_ALPHA1-6 : bond 0.02811 ( 3) link_ALPHA1-6 : angle 3.70058 ( 9) link_BETA1-4 : bond 0.00517 ( 42) link_BETA1-4 : angle 1.65976 ( 126) link_NAG-ASN : bond 0.00701 ( 45) link_NAG-ASN : angle 2.74734 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9785.31 seconds wall clock time: 167 minutes 33.45 seconds (10053.45 seconds total)