Starting phenix.real_space_refine on Thu Sep 18 23:28:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmb_47000/09_2025/9dmb_47000.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmb_47000/09_2025/9dmb_47000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dmb_47000/09_2025/9dmb_47000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmb_47000/09_2025/9dmb_47000.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dmb_47000/09_2025/9dmb_47000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmb_47000/09_2025/9dmb_47000.map" } resolution = 4.27 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= 0.010 sd= 0.083 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 129 5.16 5 C 13122 2.51 5 N 3435 2.21 5 O 4335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s 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: 21021 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 847 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "C" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1020 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 847 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "G" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1020 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 847 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "H" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1020 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "L" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "F" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "K" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" 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: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "i" 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "r" 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: "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: 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: "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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "K" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.28, per 1000 atoms: 0.25 Number of scatterers: 21021 At special positions: 0 Unit cell: (169.952, 176.447, 123.405, 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 129 16.00 O 4335 8.00 N 3435 7.00 C 13122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 605 " - pdb=" SG CYS K 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 605 " - pdb=" SG CYS L 501 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 74 " distance=2.04 Simple disulfide: pdb=" SG CYS L 119 " - pdb=" SG CYS L 205 " distance=2.04 Simple disulfide: pdb=" SG CYS L 126 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 131 " - pdb=" SG CYS L 157 " distance=2.03 Simple disulfide: pdb=" SG CYS L 201 " - pdb=" SG CYS L 433 " distance=2.03 Simple disulfide: pdb=" SG CYS L 218 " - pdb=" SG CYS L 247 " distance=2.03 Simple disulfide: pdb=" SG CYS L 228 " - pdb=" SG CYS L 239 " distance=2.03 Simple disulfide: pdb=" SG CYS L 296 " - pdb=" SG CYS L 331 " distance=2.03 Simple disulfide: pdb=" SG CYS L 378 " - pdb=" SG CYS L 445 " distance=2.03 Simple disulfide: pdb=" SG CYS L 385 " - pdb=" SG CYS L 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.04 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " " BMA c 3 " - " MAN c 4 " " BMA e 3 " - " MAN e 4 " " BMA l 3 " - " MAN l 4 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 5 " " BMA Z 3 " - " MAN Z 5 " " BMA c 3 " - " MAN c 5 " " BMA e 3 " - " MAN e 5 " " BMA l 3 " - " MAN l 5 " " BMA o 3 " - " MAN o 5 " " BMA q 3 " - " MAN q 5 " BETA1-4 " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " 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 h 2 " - " BMA h 3 " " 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 l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " 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 o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 301 " " NAG F 603 " - " ASN F 339 " " NAG F 604 " - " ASN F 355 " " NAG F 605 " - " ASN F 137 " " NAG F 606 " - " ASN F 448 " " NAG F 607 " - " ASN F 160 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 637 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 637 " " NAG K 601 " - " ASN K 88 " " NAG K 602 " - " ASN K 301 " " NAG K 603 " - " ASN K 339 " " NAG K 604 " - " ASN K 355 " " NAG K 605 " - " ASN K 137 " " NAG K 606 " - " ASN K 448 " " NAG K 607 " - " ASN K 160 " " NAG L 601 " - " ASN L 88 " " NAG L 602 " - " ASN L 301 " " NAG L 603 " - " ASN L 339 " " NAG L 604 " - " ASN L 355 " " NAG L 605 " - " ASN L 137 " " NAG L 606 " - " ASN L 448 " " NAG L 607 " - " ASN L 160 " " NAG M 1 " - " ASN L 156 " " NAG N 1 " - " ASN L 262 " " NAG O 1 " - " ASN L 332 " " NAG P 1 " - " ASN L 392 " " NAG Q 1 " - " ASN L 386 " " NAG R 1 " - " ASN L 276 " " NAG S 1 " - " ASN L 363 " " NAG T 1 " - " ASN L 197 " " NAG U 1 " - " ASN L 133 " " NAG V 1 " - " ASN L 295 " " NAG W 1 " - " ASN L 234 " " NAG X 1 " - " ASN L 462 " " NAG Y 1 " - " ASN F 156 " " NAG Z 1 " - " ASN F 262 " " NAG a 1 " - " ASN F 332 " " NAG b 1 " - " ASN F 392 " " NAG c 1 " - " ASN F 386 " " NAG d 1 " - " ASN F 276 " " NAG e 1 " - " ASN F 363 " " NAG f 1 " - " ASN F 197 " " NAG g 1 " - " ASN F 133 " " NAG h 1 " - " ASN F 295 " " NAG i 1 " - " ASN F 234 " " NAG j 1 " - " ASN F 462 " " NAG k 1 " - " ASN K 156 " " NAG l 1 " - " ASN K 262 " " NAG m 1 " - " ASN K 332 " " NAG n 1 " - " ASN K 392 " " NAG o 1 " - " ASN K 386 " " NAG p 1 " - " ASN K 276 " " NAG q 1 " - " ASN K 363 " " NAG r 1 " - " ASN K 197 " " NAG s 1 " - " ASN K 133 " " NAG t 1 " - " ASN K 295 " " NAG u 1 " - " ASN K 234 " " NAG v 1 " - " ASN K 462 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 826.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 48 sheets defined 18.0% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'C' and resid 84 through 88 removed outlier: 4.351A pdb=" N THR C 88 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 543 removed outlier: 4.521A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 595 removed outlier: 3.915A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.329A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 641 through 663 removed outlier: 3.554A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS E 655 " --> pdb=" O ASN E 651 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN E 656 " --> pdb=" O GLN E 652 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU E 660 " --> pdb=" O ASN E 656 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU E 661 " --> pdb=" O GLU E 657 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA E 662 " --> pdb=" O GLN E 658 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU E 663 " --> pdb=" O ASP E 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 88 removed outlier: 4.346A pdb=" N THR G 88 " --> pdb=" O ALA G 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 537 through 543 removed outlier: 4.514A pdb=" N ASN I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 570 through 595 removed outlier: 3.915A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 616 removed outlier: 4.325A pdb=" N SER I 615 " --> pdb=" O ASN I 611 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 641 through 663 removed outlier: 3.552A pdb=" N LEU I 645 " --> pdb=" O ILE I 641 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS I 655 " --> pdb=" O ASN I 651 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN I 656 " --> pdb=" O GLN I 652 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU I 660 " --> pdb=" O ASN I 656 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEU I 661 " --> pdb=" O GLU I 657 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA I 662 " --> pdb=" O GLN I 658 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU I 663 " --> pdb=" O ASP I 659 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 88 removed outlier: 4.352A pdb=" N THR H 88 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 543 removed outlier: 4.516A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 595 removed outlier: 3.916A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 616 removed outlier: 4.330A pdb=" N SER J 615 " --> pdb=" O ASN J 611 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 641 through 663 removed outlier: 3.552A pdb=" N LEU J 645 " --> pdb=" O ILE J 641 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS J 655 " --> pdb=" O ASN J 651 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN J 656 " --> pdb=" O GLN J 652 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU J 660 " --> pdb=" O ASN J 656 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU J 661 " --> pdb=" O GLU J 657 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA J 662 " --> pdb=" O GLN J 658 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU J 663 " --> pdb=" O ASP J 659 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 63 removed outlier: 3.894A pdb=" N THR L 63 " --> pdb=" O LYS L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 116 removed outlier: 4.267A pdb=" N GLU L 102 " --> pdb=" O ASN L 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE L 109 " --> pdb=" O HIS L 105 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU L 116 " --> pdb=" O TRP L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 126 removed outlier: 3.895A pdb=" N LEU L 125 " --> pdb=" O LEU L 122 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS L 126 " --> pdb=" O THR L 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 122 through 126' Processing helix chain 'L' and resid 139 through 152 removed outlier: 6.424A pdb=" N GLY L 152 " --> pdb=" O ASP L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 354 removed outlier: 4.014A pdb=" N LYS L 347 " --> pdb=" O GLY L 343 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN L 348 " --> pdb=" O LYS L 344 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS L 351 " --> pdb=" O LYS L 347 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS L 352 " --> pdb=" O GLN L 348 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE L 353 " --> pdb=" O LEU L 349 " (cutoff:3.500A) Processing helix chain 'L' and resid 474 through 481 removed outlier: 3.821A pdb=" N ASN L 478 " --> pdb=" O ASP L 474 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP L 479 " --> pdb=" O MET L 475 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER L 481 " --> pdb=" O ASP L 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 63 removed outlier: 3.894A pdb=" N THR F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 116 removed outlier: 4.267A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.899A pdb=" N LEU F 125 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 122 through 126' Processing helix chain 'F' and resid 139 through 152 removed outlier: 6.427A pdb=" N GLY F 152 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 354 removed outlier: 4.003A pdb=" N LYS F 347 " --> pdb=" O GLY F 343 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE F 353 " --> pdb=" O LEU F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 481 removed outlier: 3.834A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 63 removed outlier: 3.895A pdb=" N THR K 63 " --> pdb=" O LYS K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 116 removed outlier: 4.264A pdb=" N GLU K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE K 109 " --> pdb=" O HIS K 105 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU K 116 " --> pdb=" O TRP K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 126 removed outlier: 3.895A pdb=" N LEU K 125 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N CYS K 126 " --> pdb=" O THR K 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 122 through 126' Processing helix chain 'K' and resid 139 through 152 removed outlier: 6.427A pdb=" N GLY K 152 " --> pdb=" O ASP K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 354 removed outlier: 4.010A pdb=" N LYS K 347 " --> pdb=" O GLY K 343 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN K 348 " --> pdb=" O LYS K 344 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS K 351 " --> pdb=" O LYS K 347 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS K 352 " --> pdb=" O GLN K 348 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE K 353 " --> pdb=" O LEU K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 481 removed outlier: 3.820A pdb=" N ASN K 478 " --> pdb=" O ASP K 474 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.847A pdb=" N LEU A 11 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 102 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 34 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 37 " --> pdb=" O GLN A 45 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 45 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.630A pdb=" N GLN C 5 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP C 73 " --> pdb=" O GLN C 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.721A pdb=" N LEU C 12 " --> pdb=" O THR C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 46 through 50 removed outlier: 5.249A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.659A pdb=" N GLN C 101J" --> pdb=" O TRP C 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 603 through 604 removed outlier: 3.716A pdb=" N CYS E 604 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL K 38 " --> pdb=" O CYS E 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.846A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 102 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP B 34 " --> pdb=" O MET B 89 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 37 " --> pdb=" O GLN B 45 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 45 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.620A pdb=" N GLN G 5 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP G 73 " --> pdb=" O GLN G 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.724A pdb=" N LEU G 12 " --> pdb=" O THR G 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 46 through 50 removed outlier: 5.245A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 99 through 100 removed outlier: 3.657A pdb=" N GLN G 101J" --> pdb=" O TRP G 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 603 through 604 removed outlier: 3.723A pdb=" N CYS I 604 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL F 38 " --> pdb=" O CYS I 604 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.841A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP D 34 " --> pdb=" O MET D 89 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 37 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN D 45 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.631A pdb=" N GLN H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP H 73 " --> pdb=" O GLN H 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.712A pdb=" N LEU H 12 " --> pdb=" O THR H 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H' and resid 46 through 50 removed outlier: 5.244A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 99 through 100 removed outlier: 3.655A pdb=" N GLN H 101J" --> pdb=" O TRP H 100 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 603 through 604 removed outlier: 3.723A pdb=" N CYS J 604 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL L 38 " --> pdb=" O CYS J 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AC5, first strand: chain 'L' and resid 84 through 85 removed outlier: 3.856A pdb=" N ILE L 225 " --> pdb=" O VAL L 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 91 through 93 removed outlier: 3.877A pdb=" N GLU L 91 " --> pdb=" O CYS L 239 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE L 93 " --> pdb=" O GLY L 237 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY L 237 " --> pdb=" O PHE L 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 132 through 133 removed outlier: 3.823A pdb=" N THR L 132 " --> pdb=" O ASN L 156 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS L 157 " --> pdb=" O SER L 174 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN L 170 " --> pdb=" O MET L 161 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 181 through 183 removed outlier: 3.728A pdb=" N ARG L 192 " --> pdb=" O VAL L 182 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 272 through 273 removed outlier: 6.291A pdb=" N THR L 450 " --> pdb=" O PHE L 288 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N THR L 290 " --> pdb=" O ASN L 448 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N ASN L 448 " --> pdb=" O THR L 290 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL L 292 " --> pdb=" O VAL L 446 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N VAL L 446 " --> pdb=" O VAL L 292 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N ILE L 294 " --> pdb=" O ARG L 444 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N ARG L 444 " --> pdb=" O ILE L 294 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE L 358 " --> pdb=" O GLU L 466 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE L 468 " --> pdb=" O ILE L 358 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG L 360 " --> pdb=" O PHE L 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 272 through 273 removed outlier: 7.654A pdb=" N GLN L 293 " --> pdb=" O SER L 334 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER L 334 " --> pdb=" O GLN L 293 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR L 297 " --> pdb=" O HIS L 330 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS L 330 " --> pdb=" O THR L 297 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS L 331 " --> pdb=" O LEU L 416 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU L 416 " --> pdb=" O CYS L 331 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL L 333 " --> pdb=" O ILE L 414 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 304 through 312 removed outlier: 6.810A pdb=" N GLN L 315 " --> pdb=" O ILE L 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 374 through 378 removed outlier: 3.863A pdb=" N CYS L 385 " --> pdb=" O HIS L 374 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 45 through 46 Processing sheet with id=AD5, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.863A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 91 through 93 removed outlier: 3.879A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE F 93 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 132 through 133 removed outlier: 3.822A pdb=" N THR F 132 " --> pdb=" O ASN F 156 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS F 157 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN F 170 " --> pdb=" O MET F 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 181 through 183 removed outlier: 3.715A pdb=" N ARG F 192 " --> pdb=" O VAL F 182 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 272 through 273 removed outlier: 6.292A pdb=" N THR F 450 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 11.386A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 10.107A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 272 through 273 removed outlier: 7.654A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR F 297 " --> pdb=" O HIS F 330 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS F 331 " --> pdb=" O LEU F 416 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 416 " --> pdb=" O CYS F 331 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL F 333 " --> pdb=" O ILE F 414 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.810A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 374 through 378 removed outlier: 3.864A pdb=" N CYS F 385 " --> pdb=" O HIS F 374 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 45 through 46 Processing sheet with id=AE5, first strand: chain 'K' and resid 84 through 85 removed outlier: 3.860A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 91 through 93 removed outlier: 3.875A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE K 93 " --> pdb=" O GLY K 237 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY K 237 " --> pdb=" O PHE K 93 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 132 through 133 removed outlier: 3.819A pdb=" N THR K 132 " --> pdb=" O ASN K 156 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS K 157 " --> pdb=" O SER K 174 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN K 170 " --> pdb=" O MET K 161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 181 through 183 removed outlier: 3.721A pdb=" N ARG K 192 " --> pdb=" O VAL K 182 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 272 through 273 removed outlier: 6.287A pdb=" N THR K 450 " --> pdb=" O PHE K 288 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N THR K 290 " --> pdb=" O ASN K 448 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ASN K 448 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N VAL K 292 " --> pdb=" O VAL K 446 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N VAL K 446 " --> pdb=" O VAL K 292 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N ILE K 294 " --> pdb=" O ARG K 444 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N ARG K 444 " --> pdb=" O ILE K 294 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE K 358 " --> pdb=" O GLU K 466 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE K 468 " --> pdb=" O ILE K 358 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 272 through 273 removed outlier: 7.665A pdb=" N GLN K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER K 334 " --> pdb=" O GLN K 293 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR K 297 " --> pdb=" O HIS K 330 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS K 330 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS K 331 " --> pdb=" O LEU K 416 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU K 416 " --> pdb=" O CYS K 331 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL K 333 " --> pdb=" O ILE K 414 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 304 through 312 removed outlier: 6.809A pdb=" N GLN K 315 " --> pdb=" O ILE K 309 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 374 through 378 removed outlier: 3.865A pdb=" N CYS K 385 " --> pdb=" O HIS K 374 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 3.10 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: 6363 1.34 - 1.46: 5454 1.46 - 1.58: 9444 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 21435 Sorted by residual: bond pdb=" N ASP D 1 " pdb=" CA ASP D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N GLN G 1 " pdb=" CA GLN G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N GLN C 1 " pdb=" CA GLN C 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N ASP B 1 " pdb=" CA ASP B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 21430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 28559 1.64 - 3.28: 449 3.28 - 4.91: 84 4.91 - 6.55: 20 6.55 - 8.19: 6 Bond angle restraints: 29118 Sorted by residual: angle pdb=" C1 MAN N 5 " pdb=" O5 MAN N 5 " pdb=" C5 MAN N 5 " ideal model delta sigma weight residual 115.81 124.00 -8.19 3.00e+00 1.11e-01 7.46e+00 angle pdb=" C1 MAN l 5 " pdb=" O5 MAN l 5 " pdb=" C5 MAN l 5 " ideal model delta sigma weight residual 115.81 123.98 -8.17 3.00e+00 1.11e-01 7.41e+00 angle pdb=" C1 MAN Z 5 " pdb=" O5 MAN Z 5 " pdb=" C5 MAN Z 5 " ideal model delta sigma weight residual 115.81 123.95 -8.14 3.00e+00 1.11e-01 7.36e+00 angle pdb=" N VAL B 58 " pdb=" CA VAL B 58 " pdb=" C VAL B 58 " ideal model delta sigma weight residual 108.88 114.54 -5.66 2.16e+00 2.14e-01 6.86e+00 angle pdb=" N VAL A 58 " pdb=" CA VAL A 58 " pdb=" C VAL A 58 " ideal model delta sigma weight residual 108.88 114.46 -5.58 2.16e+00 2.14e-01 6.67e+00 ... (remaining 29113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 13253 17.56 - 35.12: 1109 35.12 - 52.68: 222 52.68 - 70.24: 56 70.24 - 87.80: 21 Dihedral angle restraints: 14661 sinusoidal: 7617 harmonic: 7044 Sorted by residual: dihedral pdb=" CB CYS K 119 " pdb=" SG CYS K 119 " pdb=" SG CYS K 205 " pdb=" CB CYS K 205 " ideal model delta sinusoidal sigma weight residual -86.00 -171.81 85.81 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -171.81 85.81 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS L 119 " pdb=" SG CYS L 119 " pdb=" SG CYS L 205 " pdb=" CB CYS L 205 " ideal model delta sinusoidal sigma weight residual -86.00 -171.80 85.80 1 1.00e+01 1.00e-02 8.90e+01 ... (remaining 14658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3174 0.051 - 0.102: 312 0.102 - 0.152: 195 0.152 - 0.203: 3 0.203 - 0.254: 3 Chirality restraints: 3687 Sorted by residual: chirality pdb=" C1 NAG t 1 " pdb=" ND2 ASN K 295 " pdb=" C2 NAG t 1 " pdb=" O5 NAG t 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN L 295 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN F 295 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 3684 not shown) Planarity restraints: 3561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 58 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.28e+00 pdb=" N PRO A 59 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 58 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO D 59 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 58 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO B 59 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " 0.026 5.00e-02 4.00e+02 ... (remaining 3558 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 649 2.70 - 3.25: 20084 3.25 - 3.80: 30376 3.80 - 4.35: 37456 4.35 - 4.90: 61601 Nonbonded interactions: 150166 Sorted by model distance: nonbonded pdb=" OD2 ASP L 457 " pdb=" OG1 THR L 467 " model vdw 2.144 3.040 nonbonded pdb=" OD2 ASP F 457 " pdb=" OG1 THR F 467 " model vdw 2.147 3.040 nonbonded pdb=" OD2 ASP K 457 " pdb=" OG1 THR K 467 " model vdw 2.147 3.040 nonbonded pdb=" O3 NAG d 2 " pdb=" O5 BMA d 3 " model vdw 2.195 3.040 nonbonded pdb=" O3 NAG R 2 " pdb=" O5 BMA R 3 " model vdw 2.195 3.040 ... (remaining 150161 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'g' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 's' selection = chain 'v' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'Z' selection = chain 'c' selection = chain 'e' selection = chain 'l' selection = chain 'o' selection = chain 'q' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'n' selection = chain 'p' selection = chain 'r' selection = chain 't' selection = chain 'u' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.950 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.002 0.042 21618 Z= 0.098 Angle : 0.569 8.431 29625 Z= 0.255 Chirality : 0.042 0.254 3687 Planarity : 0.003 0.045 3498 Dihedral : 12.958 87.803 9999 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.18), residues: 2406 helix: 1.09 (0.31), residues: 342 sheet: 0.23 (0.27), residues: 480 loop : -1.50 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 95 TYR 0.005 0.000 TYR G 101L PHE 0.003 0.000 PHE K 53 TRP 0.004 0.000 TRP L 338 HIS 0.001 0.000 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00207 (21435) covalent geometry : angle 0.52537 (29118) SS BOND : bond 0.00199 ( 42) SS BOND : angle 0.66369 ( 84) hydrogen bonds : bond 0.29549 ( 462) hydrogen bonds : angle 9.53475 ( 1278) link_ALPHA1-3 : bond 0.01502 ( 9) link_ALPHA1-3 : angle 2.40505 ( 27) link_ALPHA1-6 : bond 0.01293 ( 9) link_ALPHA1-6 : angle 2.16306 ( 27) link_BETA1-4 : bond 0.00582 ( 60) link_BETA1-4 : angle 2.25766 ( 180) link_NAG-ASN : bond 0.00180 ( 63) link_NAG-ASN : angle 1.28791 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 530 MET cc_start: 0.7685 (ptm) cc_final: 0.6545 (ptp) REVERT: B 14 THR cc_start: 0.8609 (m) cc_final: 0.7171 (p) REVERT: I 530 MET cc_start: 0.7434 (ptm) cc_final: 0.6697 (ptp) REVERT: J 530 MET cc_start: 0.7644 (ptm) cc_final: 0.7098 (ttp) outliers start: 3 outliers final: 3 residues processed: 181 average time/residue: 0.1850 time to fit residues: 49.7486 Evaluate side-chains 96 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 235 optimal weight: 0.0980 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 590 GLN I 590 GLN J 590 GLN L 287 GLN L 302 ASN L 425 ASN F 287 GLN F 302 ASN F 425 ASN K 287 GLN K 302 ASN K 425 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.022892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.017430 restraints weight = 305411.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.017902 restraints weight = 193696.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.018245 restraints weight = 143039.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.018480 restraints weight = 116069.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.018635 restraints weight = 100468.662| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21618 Z= 0.280 Angle : 0.895 15.179 29625 Z= 0.411 Chirality : 0.053 0.745 3687 Planarity : 0.005 0.054 3498 Dihedral : 9.610 94.226 5496 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.17), residues: 2406 helix: 0.79 (0.29), residues: 354 sheet: -0.09 (0.25), residues: 537 loop : -1.90 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 61 TYR 0.010 0.002 TYR K 318 PHE 0.029 0.003 PHE B 98 TRP 0.029 0.002 TRP K 427 HIS 0.005 0.001 HIS D 27D Details of bonding type rmsd covalent geometry : bond 0.00575 (21435) covalent geometry : angle 0.83096 (29118) SS BOND : bond 0.00268 ( 42) SS BOND : angle 1.12407 ( 84) hydrogen bonds : bond 0.05515 ( 462) hydrogen bonds : angle 6.66003 ( 1278) link_ALPHA1-3 : bond 0.01564 ( 9) link_ALPHA1-3 : angle 1.91962 ( 27) link_ALPHA1-6 : bond 0.01334 ( 9) link_ALPHA1-6 : angle 1.92705 ( 27) link_BETA1-4 : bond 0.00682 ( 60) link_BETA1-4 : angle 2.68854 ( 180) link_NAG-ASN : bond 0.00836 ( 63) link_NAG-ASN : angle 3.27022 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8560 (m-30) cc_final: 0.8349 (m-30) REVERT: A 46 LEU cc_start: 0.8508 (tt) cc_final: 0.7913 (tt) REVERT: E 535 MET cc_start: 0.9372 (mmp) cc_final: 0.8877 (mmm) REVERT: D 14 THR cc_start: 0.8447 (p) cc_final: 0.8162 (t) REVERT: D 17 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8495 (mp0) REVERT: J 535 MET cc_start: 0.9568 (tpp) cc_final: 0.9212 (tpp) REVERT: L 100 MET cc_start: 0.9692 (mtm) cc_final: 0.9286 (mtt) REVERT: L 161 MET cc_start: 0.9416 (tpt) cc_final: 0.9041 (tpp) REVERT: L 475 MET cc_start: 0.8392 (pmm) cc_final: 0.8081 (pmm) REVERT: F 100 MET cc_start: 0.9372 (mtt) cc_final: 0.9058 (mtt) REVERT: F 161 MET cc_start: 0.9405 (tpp) cc_final: 0.9145 (tpp) REVERT: F 434 MET cc_start: 0.9078 (tmm) cc_final: 0.8865 (tmm) REVERT: F 475 MET cc_start: 0.8244 (pmm) cc_final: 0.7894 (pmm) REVERT: K 100 MET cc_start: 0.9315 (mtt) cc_final: 0.8894 (mtt) REVERT: K 161 MET cc_start: 0.9519 (tpp) cc_final: 0.9312 (tpp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1780 time to fit residues: 31.0095 Evaluate side-chains 86 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 169 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.022835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.017518 restraints weight = 319075.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.018019 restraints weight = 198757.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.018372 restraints weight = 144122.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.018615 restraints weight = 115646.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.018776 restraints weight = 99316.313| |-----------------------------------------------------------------------------| r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21618 Z= 0.219 Angle : 0.793 14.974 29625 Z= 0.363 Chirality : 0.051 0.681 3687 Planarity : 0.005 0.065 3498 Dihedral : 9.289 82.894 5496 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.17), residues: 2406 helix: 0.69 (0.29), residues: 378 sheet: -0.25 (0.25), residues: 510 loop : -1.91 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 77 TYR 0.018 0.002 TYR H 101L PHE 0.027 0.002 PHE D 98 TRP 0.013 0.002 TRP J 623 HIS 0.004 0.001 HIS B 27D Details of bonding type rmsd covalent geometry : bond 0.00457 (21435) covalent geometry : angle 0.73516 (29118) SS BOND : bond 0.00541 ( 42) SS BOND : angle 1.39505 ( 84) hydrogen bonds : bond 0.04654 ( 462) hydrogen bonds : angle 5.89324 ( 1278) link_ALPHA1-3 : bond 0.01385 ( 9) link_ALPHA1-3 : angle 2.07919 ( 27) link_ALPHA1-6 : bond 0.01360 ( 9) link_ALPHA1-6 : angle 2.01106 ( 27) link_BETA1-4 : bond 0.00583 ( 60) link_BETA1-4 : angle 2.25806 ( 180) link_NAG-ASN : bond 0.00453 ( 63) link_NAG-ASN : angle 2.91308 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8754 (tt) cc_final: 0.8409 (tt) REVERT: B 34 ASP cc_start: 0.8655 (m-30) cc_final: 0.8260 (m-30) REVERT: B 46 LEU cc_start: 0.9146 (tt) cc_final: 0.8874 (tt) REVERT: B 89 MET cc_start: 0.9198 (tmm) cc_final: 0.8886 (tmm) REVERT: D 89 MET cc_start: 0.9276 (tmm) cc_final: 0.8995 (tmm) REVERT: J 535 MET cc_start: 0.9529 (tpp) cc_final: 0.9153 (tpp) REVERT: L 100 MET cc_start: 0.9691 (mtm) cc_final: 0.9198 (mtt) REVERT: L 161 MET cc_start: 0.9557 (tpt) cc_final: 0.9174 (tpp) REVERT: L 475 MET cc_start: 0.8440 (pmm) cc_final: 0.8055 (pmm) REVERT: F 161 MET cc_start: 0.9539 (tpp) cc_final: 0.9286 (tpp) REVERT: F 434 MET cc_start: 0.9137 (tmm) cc_final: 0.8838 (tmm) REVERT: F 475 MET cc_start: 0.8316 (pmm) cc_final: 0.7886 (pmm) REVERT: K 161 MET cc_start: 0.9608 (tpp) cc_final: 0.9401 (tpp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1705 time to fit residues: 26.4854 Evaluate side-chains 80 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 72 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 226 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 215 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.022241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.016810 restraints weight = 305686.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.017285 restraints weight = 194203.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.017613 restraints weight = 143274.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.017835 restraints weight = 116462.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.017987 restraints weight = 101089.887| |-----------------------------------------------------------------------------| r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21618 Z= 0.206 Angle : 0.783 13.895 29625 Z= 0.355 Chirality : 0.050 0.640 3687 Planarity : 0.005 0.060 3498 Dihedral : 9.399 84.820 5496 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.17), residues: 2406 helix: 0.82 (0.29), residues: 378 sheet: -0.62 (0.24), residues: 555 loop : -1.90 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 77 TYR 0.014 0.001 TYR G 32 PHE 0.018 0.002 PHE D 98 TRP 0.010 0.001 TRP F 427 HIS 0.005 0.001 HIS B 27D Details of bonding type rmsd covalent geometry : bond 0.00428 (21435) covalent geometry : angle 0.72587 (29118) SS BOND : bond 0.00370 ( 42) SS BOND : angle 1.15460 ( 84) hydrogen bonds : bond 0.03966 ( 462) hydrogen bonds : angle 5.58553 ( 1278) link_ALPHA1-3 : bond 0.01407 ( 9) link_ALPHA1-3 : angle 2.17424 ( 27) link_ALPHA1-6 : bond 0.01336 ( 9) link_ALPHA1-6 : angle 1.90749 ( 27) link_BETA1-4 : bond 0.00595 ( 60) link_BETA1-4 : angle 2.29896 ( 180) link_NAG-ASN : bond 0.00459 ( 63) link_NAG-ASN : angle 2.86220 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8426 (m-30) cc_final: 0.8068 (m-30) REVERT: A 46 LEU cc_start: 0.8586 (tt) cc_final: 0.8333 (tt) REVERT: A 89 MET cc_start: 0.9031 (tmm) cc_final: 0.8737 (tmm) REVERT: E 535 MET cc_start: 0.9388 (mmp) cc_final: 0.8955 (mmm) REVERT: G 22 CYS cc_start: 0.8892 (t) cc_final: 0.8594 (t) REVERT: I 530 MET cc_start: 0.8917 (ptm) cc_final: 0.8661 (ptp) REVERT: J 535 MET cc_start: 0.9488 (tpp) cc_final: 0.9121 (tpp) REVERT: L 100 MET cc_start: 0.9684 (mtm) cc_final: 0.9127 (mtt) REVERT: L 161 MET cc_start: 0.9442 (tpt) cc_final: 0.9124 (tpp) REVERT: L 475 MET cc_start: 0.8515 (pmm) cc_final: 0.8109 (pmm) REVERT: F 161 MET cc_start: 0.9412 (tpp) cc_final: 0.9177 (tpp) REVERT: F 475 MET cc_start: 0.8340 (pmm) cc_final: 0.7876 (pmm) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1578 time to fit residues: 22.7226 Evaluate side-chains 81 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 21 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 chunk 75 optimal weight: 0.3980 chunk 139 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 88 optimal weight: 0.0980 chunk 115 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.025056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.020413 restraints weight = 337607.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.021002 restraints weight = 181375.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.021398 restraints weight = 120580.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.021676 restraints weight = 91546.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.021865 restraints weight = 75356.447| |-----------------------------------------------------------------------------| r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21618 Z= 0.122 Angle : 0.742 13.170 29625 Z= 0.329 Chirality : 0.050 0.602 3687 Planarity : 0.004 0.059 3498 Dihedral : 9.179 82.266 5496 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.17), residues: 2406 helix: 1.07 (0.29), residues: 378 sheet: -0.34 (0.24), residues: 519 loop : -1.90 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 77 TYR 0.011 0.001 TYR L 486 PHE 0.013 0.001 PHE D 98 TRP 0.012 0.001 TRP C 47 HIS 0.002 0.001 HIS L 249 Details of bonding type rmsd covalent geometry : bond 0.00253 (21435) covalent geometry : angle 0.68098 (29118) SS BOND : bond 0.00299 ( 42) SS BOND : angle 1.35326 ( 84) hydrogen bonds : bond 0.03667 ( 462) hydrogen bonds : angle 5.17780 ( 1278) link_ALPHA1-3 : bond 0.01519 ( 9) link_ALPHA1-3 : angle 2.19515 ( 27) link_ALPHA1-6 : bond 0.01329 ( 9) link_ALPHA1-6 : angle 1.85736 ( 27) link_BETA1-4 : bond 0.00613 ( 60) link_BETA1-4 : angle 2.23039 ( 180) link_NAG-ASN : bond 0.00328 ( 63) link_NAG-ASN : angle 2.83739 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8342 (m-30) cc_final: 0.7933 (m-30) REVERT: A 46 LEU cc_start: 0.8472 (tt) cc_final: 0.8155 (tt) REVERT: A 89 MET cc_start: 0.9056 (tmm) cc_final: 0.8734 (tmm) REVERT: C 22 CYS cc_start: 0.8822 (t) cc_final: 0.8441 (t) REVERT: G 22 CYS cc_start: 0.8635 (t) cc_final: 0.8274 (t) REVERT: I 530 MET cc_start: 0.8868 (ptm) cc_final: 0.8627 (ptp) REVERT: J 535 MET cc_start: 0.9397 (tpp) cc_final: 0.8947 (tpp) REVERT: L 100 MET cc_start: 0.9669 (mtm) cc_final: 0.9164 (mtt) REVERT: L 161 MET cc_start: 0.9534 (tpt) cc_final: 0.9281 (tpp) REVERT: L 475 MET cc_start: 0.8457 (pmm) cc_final: 0.8064 (pmm) REVERT: F 161 MET cc_start: 0.9432 (tpp) cc_final: 0.9231 (tpp) REVERT: F 475 MET cc_start: 0.8269 (pmm) cc_final: 0.7781 (pmm) REVERT: K 161 MET cc_start: 0.9597 (tpp) cc_final: 0.9339 (tpp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1391 time to fit residues: 20.3426 Evaluate side-chains 82 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 154 optimal weight: 0.0970 chunk 140 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** I 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.021577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.016647 restraints weight = 339820.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.017115 restraints weight = 210240.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.017436 restraints weight = 152093.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.017655 restraints weight = 122206.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.017793 restraints weight = 105349.816| |-----------------------------------------------------------------------------| r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 21618 Z= 0.358 Angle : 0.954 13.990 29625 Z= 0.443 Chirality : 0.052 0.627 3687 Planarity : 0.006 0.118 3498 Dihedral : 9.604 69.069 5496 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.17), residues: 2406 helix: 0.49 (0.28), residues: 378 sheet: -0.85 (0.23), residues: 576 loop : -2.05 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 77 TYR 0.019 0.002 TYR A 86 PHE 0.023 0.004 PHE H 98 TRP 0.019 0.002 TRP C 100 HIS 0.010 0.002 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00737 (21435) covalent geometry : angle 0.89330 (29118) SS BOND : bond 0.00514 ( 42) SS BOND : angle 1.88565 ( 84) hydrogen bonds : bond 0.04394 ( 462) hydrogen bonds : angle 5.89316 ( 1278) link_ALPHA1-3 : bond 0.01084 ( 9) link_ALPHA1-3 : angle 2.41986 ( 27) link_ALPHA1-6 : bond 0.01353 ( 9) link_ALPHA1-6 : angle 1.93640 ( 27) link_BETA1-4 : bond 0.00623 ( 60) link_BETA1-4 : angle 2.40827 ( 180) link_NAG-ASN : bond 0.00864 ( 63) link_NAG-ASN : angle 3.34000 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 CYS cc_start: 0.9051 (t) cc_final: 0.8728 (t) REVERT: E 535 MET cc_start: 0.9305 (mmp) cc_final: 0.8938 (mmm) REVERT: B 34 ASP cc_start: 0.8475 (m-30) cc_final: 0.7873 (t0) REVERT: G 22 CYS cc_start: 0.8920 (t) cc_final: 0.8573 (t) REVERT: I 530 MET cc_start: 0.9003 (ptm) cc_final: 0.8752 (ptp) REVERT: J 535 MET cc_start: 0.9504 (tpp) cc_final: 0.9052 (tpp) REVERT: L 100 MET cc_start: 0.9621 (mtm) cc_final: 0.9105 (mtt) REVERT: L 161 MET cc_start: 0.9471 (tpt) cc_final: 0.9241 (tpp) REVERT: F 475 MET cc_start: 0.8552 (pmm) cc_final: 0.8141 (pmm) REVERT: K 161 MET cc_start: 0.9538 (tpp) cc_final: 0.9027 (tmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1257 time to fit residues: 17.2387 Evaluate side-chains 77 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 231 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.021892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.016663 restraints weight = 313467.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.017122 restraints weight = 196205.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.017443 restraints weight = 143962.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.017657 restraints weight = 116803.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.017803 restraints weight = 101457.409| |-----------------------------------------------------------------------------| r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21618 Z= 0.208 Angle : 0.798 12.940 29625 Z= 0.364 Chirality : 0.050 0.602 3687 Planarity : 0.005 0.064 3498 Dihedral : 9.330 65.788 5496 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.17), residues: 2406 helix: 0.99 (0.29), residues: 378 sheet: -0.58 (0.24), residues: 531 loop : -2.06 (0.14), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 95 TYR 0.023 0.002 TYR C 101L PHE 0.018 0.002 PHE D 98 TRP 0.032 0.002 TRP L 69 HIS 0.004 0.001 HIS A 27D Details of bonding type rmsd covalent geometry : bond 0.00436 (21435) covalent geometry : angle 0.74119 (29118) SS BOND : bond 0.00413 ( 42) SS BOND : angle 1.75394 ( 84) hydrogen bonds : bond 0.03849 ( 462) hydrogen bonds : angle 5.45932 ( 1278) link_ALPHA1-3 : bond 0.01363 ( 9) link_ALPHA1-3 : angle 2.41080 ( 27) link_ALPHA1-6 : bond 0.01428 ( 9) link_ALPHA1-6 : angle 1.90141 ( 27) link_BETA1-4 : bond 0.00583 ( 60) link_BETA1-4 : angle 2.15703 ( 180) link_NAG-ASN : bond 0.00409 ( 63) link_NAG-ASN : angle 2.83402 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8391 (m-30) cc_final: 0.7870 (t0) REVERT: A 89 MET cc_start: 0.8995 (tmm) cc_final: 0.8659 (tmm) REVERT: C 22 CYS cc_start: 0.8993 (t) cc_final: 0.8658 (t) REVERT: E 535 MET cc_start: 0.9290 (mmp) cc_final: 0.8915 (mmm) REVERT: B 34 ASP cc_start: 0.8384 (m-30) cc_final: 0.7922 (t0) REVERT: G 22 CYS cc_start: 0.8892 (t) cc_final: 0.8543 (t) REVERT: I 530 MET cc_start: 0.9009 (ptm) cc_final: 0.8743 (ptp) REVERT: D 34 ASP cc_start: 0.8632 (m-30) cc_final: 0.8187 (t0) REVERT: J 535 MET cc_start: 0.9466 (tpp) cc_final: 0.9001 (tpp) REVERT: L 100 MET cc_start: 0.9680 (mtm) cc_final: 0.9164 (mtt) REVERT: L 161 MET cc_start: 0.9415 (tpt) cc_final: 0.9208 (tpp) REVERT: F 475 MET cc_start: 0.7940 (pmm) cc_final: 0.7479 (pmm) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1290 time to fit residues: 17.1210 Evaluate side-chains 74 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 129 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101JGLN ** I 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.021845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.016606 restraints weight = 313077.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.017061 restraints weight = 198068.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.017372 restraints weight = 145290.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.017587 restraints weight = 118374.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.017735 restraints weight = 102893.274| |-----------------------------------------------------------------------------| r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21618 Z= 0.223 Angle : 0.817 12.787 29625 Z= 0.371 Chirality : 0.050 0.588 3687 Planarity : 0.005 0.083 3498 Dihedral : 9.198 59.872 5496 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.17), residues: 2406 helix: 0.68 (0.28), residues: 399 sheet: -0.90 (0.23), residues: 567 loop : -2.12 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 579 TYR 0.023 0.002 TYR H 101L PHE 0.016 0.002 PHE B 98 TRP 0.021 0.002 TRP H 104 HIS 0.006 0.001 HIS A 27D Details of bonding type rmsd covalent geometry : bond 0.00466 (21435) covalent geometry : angle 0.76132 (29118) SS BOND : bond 0.00392 ( 42) SS BOND : angle 1.60772 ( 84) hydrogen bonds : bond 0.03842 ( 462) hydrogen bonds : angle 5.48722 ( 1278) link_ALPHA1-3 : bond 0.01246 ( 9) link_ALPHA1-3 : angle 2.45181 ( 27) link_ALPHA1-6 : bond 0.01494 ( 9) link_ALPHA1-6 : angle 1.87444 ( 27) link_BETA1-4 : bond 0.00588 ( 60) link_BETA1-4 : angle 2.22943 ( 180) link_NAG-ASN : bond 0.00468 ( 63) link_NAG-ASN : angle 2.86051 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 CYS cc_start: 0.8968 (t) cc_final: 0.8639 (t) REVERT: E 535 MET cc_start: 0.9273 (mmp) cc_final: 0.8911 (mmm) REVERT: B 34 ASP cc_start: 0.8381 (m-30) cc_final: 0.7719 (t0) REVERT: B 89 MET cc_start: 0.9059 (tmm) cc_final: 0.8813 (tmm) REVERT: G 22 CYS cc_start: 0.8888 (t) cc_final: 0.8549 (t) REVERT: I 530 MET cc_start: 0.9034 (ptm) cc_final: 0.8721 (ptp) REVERT: D 34 ASP cc_start: 0.8621 (m-30) cc_final: 0.8104 (t0) REVERT: D 89 MET cc_start: 0.9000 (tmm) cc_final: 0.8602 (tmm) REVERT: H 22 CYS cc_start: 0.9025 (t) cc_final: 0.8686 (t) REVERT: J 535 MET cc_start: 0.9457 (tpp) cc_final: 0.8993 (tpp) REVERT: L 100 MET cc_start: 0.9656 (mtm) cc_final: 0.9127 (mtt) REVERT: F 475 MET cc_start: 0.8001 (pmm) cc_final: 0.7535 (pmm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1219 time to fit residues: 16.7985 Evaluate side-chains 73 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 107 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 226 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 160 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 211 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 101JGLN ** I 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101JGLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.022300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.016934 restraints weight = 301779.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.017404 restraints weight = 190041.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.017743 restraints weight = 139112.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.017966 restraints weight = 112703.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.018112 restraints weight = 97339.421| |-----------------------------------------------------------------------------| r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21618 Z= 0.150 Angle : 0.761 12.235 29625 Z= 0.342 Chirality : 0.049 0.569 3687 Planarity : 0.005 0.068 3498 Dihedral : 8.871 59.946 5496 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.17), residues: 2406 helix: 1.01 (0.29), residues: 399 sheet: -0.88 (0.23), residues: 558 loop : -2.08 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 298 TYR 0.015 0.001 TYR C 101L PHE 0.020 0.002 PHE D 98 TRP 0.019 0.002 TRP F 69 HIS 0.002 0.001 HIS L 105 Details of bonding type rmsd covalent geometry : bond 0.00319 (21435) covalent geometry : angle 0.70712 (29118) SS BOND : bond 0.00384 ( 42) SS BOND : angle 1.29757 ( 84) hydrogen bonds : bond 0.03551 ( 462) hydrogen bonds : angle 5.19699 ( 1278) link_ALPHA1-3 : bond 0.01324 ( 9) link_ALPHA1-3 : angle 2.49624 ( 27) link_ALPHA1-6 : bond 0.01502 ( 9) link_ALPHA1-6 : angle 1.81129 ( 27) link_BETA1-4 : bond 0.00611 ( 60) link_BETA1-4 : angle 2.19678 ( 180) link_NAG-ASN : bond 0.00311 ( 63) link_NAG-ASN : angle 2.63606 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 CYS cc_start: 0.8917 (t) cc_final: 0.8578 (t) REVERT: E 535 MET cc_start: 0.9263 (mmp) cc_final: 0.8905 (mmm) REVERT: B 34 ASP cc_start: 0.8346 (m-30) cc_final: 0.7832 (t0) REVERT: G 22 CYS cc_start: 0.8866 (t) cc_final: 0.8522 (t) REVERT: I 530 MET cc_start: 0.9024 (ptm) cc_final: 0.8762 (ptp) REVERT: D 34 ASP cc_start: 0.8558 (m-30) cc_final: 0.8003 (t0) REVERT: D 89 MET cc_start: 0.8914 (tmm) cc_final: 0.8645 (tmm) REVERT: H 22 CYS cc_start: 0.8971 (t) cc_final: 0.8623 (t) REVERT: J 535 MET cc_start: 0.9447 (tpp) cc_final: 0.8987 (tpp) REVERT: L 100 MET cc_start: 0.9696 (mtm) cc_final: 0.9167 (mtt) REVERT: L 161 MET cc_start: 0.9412 (tpp) cc_final: 0.9207 (tpp) REVERT: F 475 MET cc_start: 0.7951 (pmm) cc_final: 0.7488 (pmm) REVERT: K 161 MET cc_start: 0.9546 (tpp) cc_final: 0.9312 (tpp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1296 time to fit residues: 17.3943 Evaluate side-chains 73 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 152 optimal weight: 8.9990 chunk 230 optimal weight: 8.9990 chunk 215 optimal weight: 0.0870 chunk 242 optimal weight: 0.4980 chunk 199 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 chunk 160 optimal weight: 0.9980 chunk 225 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 overall best weight: 2.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.022188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.016862 restraints weight = 312605.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.017336 restraints weight = 195533.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.017655 restraints weight = 143417.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.017877 restraints weight = 116125.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.018027 restraints weight = 100582.813| |-----------------------------------------------------------------------------| r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21618 Z= 0.168 Angle : 0.765 12.205 29625 Z= 0.345 Chirality : 0.049 0.563 3687 Planarity : 0.005 0.067 3498 Dihedral : 8.712 59.991 5496 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.17), residues: 2406 helix: 1.02 (0.29), residues: 399 sheet: -0.88 (0.23), residues: 558 loop : -2.07 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 298 TYR 0.018 0.001 TYR H 101L PHE 0.018 0.002 PHE D 98 TRP 0.019 0.002 TRP L 69 HIS 0.004 0.001 HIS A 27D Details of bonding type rmsd covalent geometry : bond 0.00355 (21435) covalent geometry : angle 0.71091 (29118) SS BOND : bond 0.00369 ( 42) SS BOND : angle 1.24795 ( 84) hydrogen bonds : bond 0.03444 ( 462) hydrogen bonds : angle 5.17280 ( 1278) link_ALPHA1-3 : bond 0.01211 ( 9) link_ALPHA1-3 : angle 2.50066 ( 27) link_ALPHA1-6 : bond 0.01538 ( 9) link_ALPHA1-6 : angle 1.73657 ( 27) link_BETA1-4 : bond 0.00606 ( 60) link_BETA1-4 : angle 2.23958 ( 180) link_NAG-ASN : bond 0.00344 ( 63) link_NAG-ASN : angle 2.64396 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4812 Ramachandran restraints generated. 2406 Oldfield, 0 Emsley, 2406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.8711 (m-10) cc_final: 0.8508 (m-10) REVERT: C 22 CYS cc_start: 0.8929 (t) cc_final: 0.8592 (t) REVERT: E 535 MET cc_start: 0.9252 (mmp) cc_final: 0.8902 (mmm) REVERT: B 34 ASP cc_start: 0.8303 (m-30) cc_final: 0.7613 (t0) REVERT: B 46 LEU cc_start: 0.9104 (tt) cc_final: 0.8772 (tt) REVERT: B 79 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8362 (mm-30) REVERT: G 22 CYS cc_start: 0.8872 (t) cc_final: 0.8530 (t) REVERT: I 530 MET cc_start: 0.9014 (ptm) cc_final: 0.8779 (ptp) REVERT: D 34 ASP cc_start: 0.8567 (m-30) cc_final: 0.8009 (t0) REVERT: D 89 MET cc_start: 0.9016 (tmm) cc_final: 0.8708 (tmm) REVERT: H 22 CYS cc_start: 0.8976 (t) cc_final: 0.8624 (t) REVERT: J 535 MET cc_start: 0.9451 (tpp) cc_final: 0.8981 (tpp) REVERT: L 100 MET cc_start: 0.9677 (mtm) cc_final: 0.9140 (mtt) REVERT: F 475 MET cc_start: 0.8024 (pmm) cc_final: 0.7567 (pmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1279 time to fit residues: 16.3357 Evaluate side-chains 75 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 101 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.023702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.019253 restraints weight = 345456.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.019804 restraints weight = 189296.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.020174 restraints weight = 127195.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.020381 restraints weight = 97239.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.020573 restraints weight = 83010.276| |-----------------------------------------------------------------------------| r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21618 Z= 0.198 Angle : 0.781 12.170 29625 Z= 0.355 Chirality : 0.049 0.564 3687 Planarity : 0.005 0.066 3498 Dihedral : 8.645 59.876 5496 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.17), residues: 2406 helix: 0.90 (0.28), residues: 399 sheet: -1.03 (0.23), residues: 579 loop : -2.06 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 298 TYR 0.016 0.001 TYR H 101L PHE 0.025 0.002 PHE A 96 TRP 0.020 0.002 TRP K 69 HIS 0.005 0.001 HIS A 27D Details of bonding type rmsd covalent geometry : bond 0.00417 (21435) covalent geometry : angle 0.72647 (29118) SS BOND : bond 0.00382 ( 42) SS BOND : angle 1.33785 ( 84) hydrogen bonds : bond 0.03487 ( 462) hydrogen bonds : angle 5.24731 ( 1278) link_ALPHA1-3 : bond 0.01131 ( 9) link_ALPHA1-3 : angle 2.52805 ( 27) link_ALPHA1-6 : bond 0.01479 ( 9) link_ALPHA1-6 : angle 1.68619 ( 27) link_BETA1-4 : bond 0.00611 ( 60) link_BETA1-4 : angle 2.27002 ( 180) link_NAG-ASN : bond 0.00407 ( 63) link_NAG-ASN : angle 2.69031 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2575.79 seconds wall clock time: 46 minutes 9.07 seconds (2769.07 seconds total)