Starting phenix.real_space_refine on Thu Mar 5 21:06:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kde_22820/03_2026/7kde_22820_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kde_22820/03_2026/7kde_22820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kde_22820/03_2026/7kde_22820_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kde_22820/03_2026/7kde_22820_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kde_22820/03_2026/7kde_22820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kde_22820/03_2026/7kde_22820.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 132 5.16 5 C 15941 2.51 5 N 4195 2.21 5 O 5219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25487 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "B" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain breaks: 5 Chain: "F" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain breaks: 5 Chain: "G" Number of atoms: 3378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3378 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain breaks: 5 Chain: "H" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1023 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "J" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1023 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "M" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1023 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "O" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 970 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 790 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "Q" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 970 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 790 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "S" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 970 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "T" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 790 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 1 Chain: "L" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 1 Chain: "N" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 1 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "X" 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: "Y" 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: "Z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "G" 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: 5.93, per 1000 atoms: 0.23 Number of scatterers: 25487 At special positions: 0 Unit cell: (170.43, 158.769, 181.194, 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 132 16.00 O 5219 8.00 N 4195 7.00 C 15941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.04 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.05 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.05 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=2.02 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 G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.05 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 87 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 5 " - " MAN Z 6 " " MAN c 4 " - " MAN c 5 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN j 4 " - " MAN j 5 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " MAN W 7 " - " MAN W 8 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " MAN j 6 " - " MAN j 7 " " BMA l 3 " - " MAN l 4 " " BMA n 3 " - " MAN n 4 " ALPHA1-6 " BMA W 3 " - " MAN W 7 " " MAN W 7 " - " MAN W 9 " " BMA Z 3 " - " MAN Z 7 " " BMA c 3 " - " MAN c 6 " " MAN c 6 " - " MAN c 8 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 7 " " BMA i 3 " - " MAN i 5 " " BMA j 3 " - " MAN j 6 " " MAN j 6 " - " MAN j 8 " " BMA l 3 " - " MAN l 5 " " BMA n 3 " - " MAN n 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG K 1 " - " NAG K 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG 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 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 i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG 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 p 1 " - " NAG p 2 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG K 1 " - " FUC K 3 " NAG-ASN " NAG A 701 " - " ASN A 618 " " NAG A 702 " - " ASN A 611 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG D 1 " - " ASN A 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 363 " " NAG E 609 " - " ASN E 392 " " NAG E 610 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 160 " " NAG F 604 " - " ASN F 197 " " NAG F 605 " - " ASN F 295 " " NAG F 606 " - " ASN F 301 " " NAG F 607 " - " ASN F 339 " " NAG F 608 " - " ASN F 355 " " NAG F 609 " - " ASN F 363 " " NAG F 610 " - " ASN F 392 " " NAG F 611 " - " ASN F 448 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 160 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 301 " " NAG G 605 " - " ASN G 339 " " NAG G 606 " - " ASN G 363 " " NAG G 607 " - " ASN G 392 " " NAG K 1 " - " ASN B 637 " " NAG U 1 " - " ASN C 637 " " NAG V 1 " - " ASN E 156 " " NAG W 1 " - " ASN E 234 " " NAG X 1 " - " ASN E 262 " " NAG Y 1 " - " ASN E 276 " " NAG Z 1 " - " ASN E 332 " " NAG a 1 " - " ASN E 386 " " NAG b 1 " - " ASN F 156 " " NAG c 1 " - " ASN F 234 " " NAG d 1 " - " ASN F 262 " " NAG e 1 " - " ASN F 276 " " NAG f 1 " - " ASN F 332 " " NAG g 1 " - " ASN F 386 " " NAG h 1 " - " ASN G 133 " " NAG i 1 " - " ASN G 156 " " NAG j 1 " - " ASN G 234 " " NAG k 1 " - " ASN G 262 " " NAG l 1 " - " ASN G 276 " " NAG m 1 " - " ASN G 295 " " NAG n 1 " - " ASN G 332 " " NAG o 1 " - " ASN G 386 " " NAG p 1 " - " ASN G 448 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 940.4 milliseconds 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5646 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 73 sheets defined 12.6% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.529A pdb=" N ALA A 533 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 534 " --> pdb=" O GLY A 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 530 through 534' Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.886A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.695A pdb=" N GLU A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 removed outlier: 3.920A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.792A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 663 removed outlier: 3.522A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.234A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 597 removed outlier: 3.668A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.212A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.600A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 542 removed outlier: 4.493A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 542 " --> pdb=" O THR C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 574 removed outlier: 3.597A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 570 through 574' Processing helix chain 'C' and resid 579 through 596 removed outlier: 3.825A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 584 " --> pdb=" O VAL C 580 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 591 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 622 Processing helix chain 'C' and resid 627 through 635 removed outlier: 4.299A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 663 removed outlier: 3.848A pdb=" N ILE C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS C 655 " --> pdb=" O ASN C 651 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 662 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU C 663 " --> pdb=" O ASP C 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.523A pdb=" N GLN E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 342 through 351 removed outlier: 3.825A pdb=" N VAL E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 4.111A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 removed outlier: 4.276A pdb=" N THR F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.784A pdb=" N LEU F 125 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 350 removed outlier: 3.591A pdb=" N VAL F 346 " --> pdb=" O LEU F 342 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS F 347 " --> pdb=" O GLY F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 475 through 480 removed outlier: 4.155A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 113 removed outlier: 3.863A pdb=" N THR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.529A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 334 through 350 removed outlier: 3.602A pdb=" N VAL G 346 " --> pdb=" O LEU G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 4.061A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.921A pdb=" N THR J 87 " --> pdb=" O ASP J 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.672A pdb=" N THR M 87 " --> pdb=" O ASP M 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 removed outlier: 4.159A pdb=" N THR O 87 " --> pdb=" O SER O 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.997A pdb=" N PHE P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 87 removed outlier: 4.127A pdb=" N THR Q 87 " --> pdb=" O SER Q 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.612A pdb=" N PHE T 83 " --> pdb=" O ALA T 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 82 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.594A pdb=" N ASP L 81 " --> pdb=" O GLN L 78 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU L 82 " --> pdb=" O THR L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 82' Processing helix chain 'N' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.617A pdb=" N THR A 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL E 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.577A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 603 through 609 removed outlier: 8.226A pdb=" N CYS C 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N TYR F 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR C 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL F 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL C 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.693A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 66 through 67 removed outlier: 7.475A pdb=" N HIS E 66 " --> pdb=" O SER E 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.888A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 170 through 177 removed outlier: 3.748A pdb=" N THR E 132 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 271 through 274 removed outlier: 3.500A pdb=" N LEU E 454 " --> pdb=" O ILE E 284 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 292 through 294 Processing sheet with id=AB1, first strand: chain 'E' and resid 307 through 312 removed outlier: 3.688A pdb=" N ILE E 309 " --> pdb=" O GLN E 315 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 329 through 334 removed outlier: 4.210A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS E 378 " --> pdb=" O GLU E 381 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'F' and resid 66 through 67 removed outlier: 6.784A pdb=" N HIS F 66 " --> pdb=" O SER F 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AB6, first strand: chain 'F' and resid 91 through 94 removed outlier: 4.063A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE F 93 " --> pdb=" O GLY F 237 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 129 through 131 removed outlier: 3.576A pdb=" N CYS F 131 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS F 189 " --> pdb=" O CYS F 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 154 through 155 Processing sheet with id=AB9, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AC1, first strand: chain 'F' and resid 200 through 203 removed outlier: 6.634A pdb=" N ALA F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N TYR F 435 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.671A pdb=" N ILE F 284 " --> pdb=" O LEU F 454 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 416 through 418 removed outlier: 3.518A pdb=" N CYS F 331 " --> pdb=" O LEU F 416 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 304 through 308 Processing sheet with id=AC5, first strand: chain 'F' and resid 358 through 360 Processing sheet with id=AC6, first strand: chain 'F' and resid 374 through 378 removed outlier: 3.944A pdb=" N CYS F 385 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS F 378 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'G' and resid 66 through 67 removed outlier: 7.103A pdb=" N HIS G 66 " --> pdb=" O SER G 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 84 through 86 removed outlier: 3.642A pdb=" N LEU G 86 " --> pdb=" O VAL G 242 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.966A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 129 through 131 removed outlier: 3.608A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 154 through 155 removed outlier: 3.500A pdb=" N PHE G 176 " --> pdb=" O LYS G 155 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AD5, first strand: chain 'G' and resid 259 through 261 removed outlier: 5.734A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE G 284 " --> pdb=" O LEU G 454 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 259 through 261 removed outlier: 5.734A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 374 through 375 removed outlier: 3.529A pdb=" N LEU G 416 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS G 331 " --> pdb=" O LEU G 416 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 304 through 307 Processing sheet with id=AD9, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AE1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.567A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.501A pdb=" N LEU H 18 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 47 through 50 removed outlier: 5.702A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG H 94 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 47 through 50 removed outlier: 5.702A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.608A pdb=" N SER J 7 " --> pdb=" O THR J 21 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU J 18 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 12 through 13 removed outlier: 6.656A pdb=" N VAL J 12 " --> pdb=" O SER J 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'J' and resid 47 through 50 removed outlier: 4.934A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG J 94 " --> pdb=" O PHE J 102 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 47 through 50 removed outlier: 4.934A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA J 88 " --> pdb=" O VAL J 109 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL J 109 " --> pdb=" O ALA J 88 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AF1, first strand: chain 'M' and resid 47 through 50 removed outlier: 5.371A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 3 through 6 removed outlier: 3.589A pdb=" N GLU O 81 " --> pdb=" O LEU O 68 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU O 68 " --> pdb=" O GLU O 81 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.826A pdb=" N VAL O 35 " --> pdb=" O GLN O 50 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN O 50 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AF5, first strand: chain 'O' and resid 100E through 100F removed outlier: 3.628A pdb=" N VAL O 100I" --> pdb=" O HIS O 100F" (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 11 through 12 removed outlier: 6.795A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AF8, first strand: chain 'P' and resid 48 through 49 Processing sheet with id=AF9, first strand: chain 'Q' and resid 3 through 6 removed outlier: 3.511A pdb=" N VAL Q 18 " --> pdb=" O ILE Q 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER Q 70 " --> pdb=" O SER Q 79 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 10 through 12 removed outlier: 3.510A pdb=" N GLU Q 10 " --> pdb=" O LEU Q 108 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA Q 88 " --> pdb=" O ILE Q 109 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N TYR Q 33 " --> pdb=" O TRP Q 52 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TRP Q 52 " --> pdb=" O TYR Q 33 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL Q 35 " --> pdb=" O GLN Q 50 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN Q 50 " --> pdb=" O VAL Q 35 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 10 through 12 removed outlier: 3.510A pdb=" N GLU Q 10 " --> pdb=" O LEU Q 108 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA Q 88 " --> pdb=" O ILE Q 109 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Q' and resid 100E through 100F removed outlier: 3.564A pdb=" N VAL Q 100I" --> pdb=" O HIS Q 100F" (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'R' and resid 5 through 7 removed outlier: 3.937A pdb=" N ARG R 24 " --> pdb=" O THR R 5 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR R 72 " --> pdb=" O SER R 65 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 11 through 12 removed outlier: 7.446A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'R' and resid 33 through 35 Processing sheet with id=AG7, first strand: chain 'R' and resid 48 through 49 Processing sheet with id=AG8, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AG9, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.517A pdb=" N ALA S 88 " --> pdb=" O ILE S 109 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL S 35 " --> pdb=" O GLN S 50 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN S 50 " --> pdb=" O VAL S 35 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP S 36 " --> pdb=" O ILE S 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'T' and resid 5 through 7 removed outlier: 3.809A pdb=" N ARG T 24 " --> pdb=" O THR T 5 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR T 72 " --> pdb=" O SER T 65 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'T' and resid 10 through 12 removed outlier: 3.766A pdb=" N THR T 102 " --> pdb=" O PHE T 86 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE T 86 " --> pdb=" O THR T 102 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'T' and resid 33 through 35 Processing sheet with id=AH4, first strand: chain 'T' and resid 48 through 49 Processing sheet with id=AH5, first strand: chain 'I' and resid 17 through 21 removed outlier: 3.556A pdb=" N VAL I 18 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 44 through 47 removed outlier: 5.677A pdb=" N LEU I 45 " --> pdb=" O GLN I 36 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN I 36 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 17 through 21 Processing sheet with id=AH8, first strand: chain 'L' and resid 44 through 47 removed outlier: 5.727A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 17 through 21 removed outlier: 3.805A pdb=" N VAL N 18 " --> pdb=" O ILE N 74 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'N' and resid 44 through 47 removed outlier: 6.666A pdb=" N TRP N 34 " --> pdb=" O LEU N 46 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1500 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: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7927 1.35 - 1.48: 7313 1.48 - 1.61: 10595 1.61 - 1.74: 0 1.74 - 1.87: 174 Bond restraints: 26009 Sorted by residual: bond pdb=" C1 MAN e 5 " pdb=" C2 MAN e 5 " ideal model delta sigma weight residual 1.526 1.594 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1 BMA e 3 " pdb=" C2 BMA e 3 " ideal model delta sigma weight residual 1.519 1.585 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C PHE G 468 " pdb=" N ARG G 469 " ideal model delta sigma weight residual 1.331 1.249 0.082 2.83e-02 1.25e+03 8.46e+00 bond pdb=" C1 NAG e 1 " pdb=" O5 NAG e 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C ASN F 195 " pdb=" N CYS F 196 " ideal model delta sigma weight residual 1.332 1.300 0.033 1.40e-02 5.10e+03 5.51e+00 ... (remaining 26004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 34519 2.96 - 5.92: 696 5.92 - 8.88: 127 8.88 - 11.85: 13 11.85 - 14.81: 2 Bond angle restraints: 35357 Sorted by residual: angle pdb=" C ALA G 204 " pdb=" N CYS G 205 " pdb=" CA CYS G 205 " ideal model delta sigma weight residual 122.48 107.69 14.79 1.77e+00 3.19e-01 6.98e+01 angle pdb=" N ILE F 277 " pdb=" CA ILE F 277 " pdb=" C ILE F 277 " ideal model delta sigma weight residual 113.53 105.71 7.82 9.80e-01 1.04e+00 6.36e+01 angle pdb=" C ALA F 204 " pdb=" N CYS F 205 " pdb=" CA CYS F 205 " ideal model delta sigma weight residual 122.56 113.24 9.32 1.34e+00 5.57e-01 4.84e+01 angle pdb=" N SER J 79 " pdb=" CA SER J 79 " pdb=" C SER J 79 " ideal model delta sigma weight residual 110.91 118.80 -7.89 1.17e+00 7.31e-01 4.54e+01 angle pdb=" N LEU L 94 " pdb=" CA LEU L 94 " pdb=" CB LEU L 94 " ideal model delta sigma weight residual 114.17 107.24 6.93 1.14e+00 7.69e-01 3.69e+01 ... (remaining 35352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.05: 15811 24.05 - 48.10: 907 48.10 - 72.15: 196 72.15 - 96.20: 100 96.20 - 120.25: 59 Dihedral angle restraints: 17073 sinusoidal: 8286 harmonic: 8787 Sorted by residual: dihedral pdb=" CA ASP I 49 " pdb=" C ASP I 49 " pdb=" N ASN I 50 " pdb=" CA ASN I 50 " ideal model delta harmonic sigma weight residual 180.00 -129.95 -50.05 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA ASP L 49 " pdb=" C ASP L 49 " pdb=" N ASN L 50 " pdb=" CA ASN L 50 " ideal model delta harmonic sigma weight residual 180.00 -130.53 -49.47 0 5.00e+00 4.00e-02 9.79e+01 dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual -86.00 0.35 -86.35 1 1.00e+01 1.00e-02 8.99e+01 ... (remaining 17070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4181 0.123 - 0.246: 164 0.246 - 0.369: 14 0.369 - 0.492: 3 0.492 - 0.615: 1 Chirality restraints: 4363 Sorted by residual: chirality pdb=" C1 NAG G 604 " pdb=" ND2 ASN G 301 " pdb=" C2 NAG G 604 " pdb=" O5 NAG G 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.44e+00 chirality pdb=" C1 NAG e 1 " pdb=" ND2 ASN F 276 " pdb=" C2 NAG e 1 " pdb=" O5 NAG e 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.84 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN F 156 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 4360 not shown) Planarity restraints: 4358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 276 " -0.017 2.00e-02 2.50e+03 5.54e-02 3.83e+01 pdb=" CG ASN F 276 " 0.076 2.00e-02 2.50e+03 pdb=" OD1 ASN F 276 " -0.063 2.00e-02 2.50e+03 pdb=" ND2 ASN F 276 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG e 1 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 276 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" CG ASN F 276 " 0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN F 276 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN F 276 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA N 13 " -0.052 5.00e-02 4.00e+02 7.71e-02 9.51e+00 pdb=" N PRO N 14 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.043 5.00e-02 4.00e+02 ... (remaining 4355 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 620 2.66 - 3.22: 23200 3.22 - 3.78: 34166 3.78 - 4.34: 47620 4.34 - 4.90: 82502 Nonbonded interactions: 188108 Sorted by model distance: nonbonded pdb=" OH TYR R 36 " pdb=" OE1 GLN R 89 " model vdw 2.097 3.040 nonbonded pdb=" NH2 ARG Q 64 " pdb=" O2 MAN c 8 " model vdw 2.101 3.120 nonbonded pdb=" O ASN O 35A" pdb=" OG1 THR O 93 " model vdw 2.112 3.040 nonbonded pdb=" OH TYR P 36 " pdb=" OE1 GLN P 89 " model vdw 2.116 3.040 nonbonded pdb=" NZ LYS G 232 " pdb=" OE1 GLU G 268 " model vdw 2.132 3.120 ... (remaining 188103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 3) selection = (chain 'V' and resid 1 through 3) selection = (chain 'b' and resid 1 through 3) } ncs_group { reference = (chain 'E' and resid 34 through 607) selection = (chain 'F' and resid 34 through 607) selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'N' } ncs_group { reference = (chain 'K' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = (chain 'W' and (resid 2 or resid 5 through 9)) selection = (chain 'c' and (resid 1 or resid 4 through 8)) selection = (chain 'j' and (resid 1 or resid 4 through 8)) } ncs_group { reference = (chain 'Z' and (resid 2 or resid 5 through 7)) selection = (chain 'f' and (resid 2 or resid 5 through 7)) selection = (chain 'n' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'e' selection = chain 'i' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.240 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.009 0.082 26188 Z= 0.380 Angle : 1.114 22.966 35849 Z= 0.557 Chirality : 0.061 0.615 4363 Planarity : 0.005 0.077 4300 Dihedral : 17.735 120.248 11292 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.47 % Favored : 87.13 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.14), residues: 2991 helix: -4.22 (0.16), residues: 351 sheet: -1.51 (0.18), residues: 921 loop : -2.52 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 24 TYR 0.032 0.002 TYR M 52 PHE 0.028 0.002 PHE F 159 TRP 0.025 0.002 TRP J 36 HIS 0.008 0.002 HIS O 100F Details of bonding type rmsd covalent geometry : bond 0.00873 (26009) covalent geometry : angle 1.06012 (35357) SS BOND : bond 0.00821 ( 45) SS BOND : angle 3.11351 ( 90) hydrogen bonds : bond 0.29491 ( 567) hydrogen bonds : angle 10.33121 ( 1500) link_ALPHA1-2 : bond 0.00311 ( 9) link_ALPHA1-2 : angle 2.45475 ( 27) link_ALPHA1-3 : bond 0.00373 ( 14) link_ALPHA1-3 : angle 2.07254 ( 42) link_ALPHA1-6 : bond 0.00382 ( 12) link_ALPHA1-6 : angle 2.12968 ( 36) link_BETA1-4 : bond 0.00658 ( 39) link_BETA1-4 : angle 2.60103 ( 117) link_BETA1-6 : bond 0.00365 ( 2) link_BETA1-6 : angle 1.76182 ( 6) link_NAG-ASN : bond 0.00513 ( 58) link_NAG-ASN : angle 3.80953 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.9148 (mtt) cc_final: 0.8641 (mtt) REVERT: E 72 HIS cc_start: 0.5823 (p90) cc_final: 0.5332 (p90) REVERT: E 342 LEU cc_start: 0.9140 (tp) cc_final: 0.8857 (tt) REVERT: F 342 LEU cc_start: 0.9211 (tp) cc_final: 0.8965 (tp) REVERT: M 91 TYR cc_start: 0.6585 (m-80) cc_final: 0.6381 (m-10) REVERT: P 61 ARG cc_start: 0.8306 (mtm110) cc_final: 0.8083 (mtm110) REVERT: Q 10 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7671 (tm-30) REVERT: S 86 ASP cc_start: 0.8284 (m-30) cc_final: 0.8038 (m-30) REVERT: T 27 GLN cc_start: 0.8304 (mt0) cc_final: 0.7971 (pt0) REVERT: I 53 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7516 (ttp80) REVERT: L 20 ILE cc_start: 0.7841 (mm) cc_final: 0.7588 (mm) REVERT: N 84 ASP cc_start: 0.7175 (m-30) cc_final: 0.6698 (t0) REVERT: N 86 TYR cc_start: 0.6712 (m-80) cc_final: 0.6439 (m-80) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.1686 time to fit residues: 96.2852 Evaluate side-chains 297 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 HIS I 6 GLN N 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116777 restraints weight = 39736.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115971 restraints weight = 28924.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117248 restraints weight = 27024.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117794 restraints weight = 20124.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118022 restraints weight = 18662.014| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26188 Z= 0.143 Angle : 0.797 14.959 35849 Z= 0.392 Chirality : 0.050 0.294 4363 Planarity : 0.005 0.063 4300 Dihedral : 14.336 109.492 5982 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.52 % Favored : 92.14 % Rotamer: Outliers : 1.27 % Allowed : 7.88 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.14), residues: 2991 helix: -3.38 (0.20), residues: 369 sheet: -1.15 (0.18), residues: 924 loop : -2.26 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 66 TYR 0.030 0.001 TYR M 52 PHE 0.012 0.001 PHE S 91 TRP 0.020 0.001 TRP M 47 HIS 0.004 0.001 HIS O 100F Details of bonding type rmsd covalent geometry : bond 0.00306 (26009) covalent geometry : angle 0.75844 (35357) SS BOND : bond 0.00631 ( 45) SS BOND : angle 1.42682 ( 90) hydrogen bonds : bond 0.04805 ( 567) hydrogen bonds : angle 6.41166 ( 1500) link_ALPHA1-2 : bond 0.00577 ( 9) link_ALPHA1-2 : angle 1.94774 ( 27) link_ALPHA1-3 : bond 0.00950 ( 14) link_ALPHA1-3 : angle 1.76799 ( 42) link_ALPHA1-6 : bond 0.00695 ( 12) link_ALPHA1-6 : angle 2.17954 ( 36) link_BETA1-4 : bond 0.00547 ( 39) link_BETA1-4 : angle 1.89208 ( 117) link_BETA1-6 : bond 0.00468 ( 2) link_BETA1-6 : angle 1.33010 ( 6) link_NAG-ASN : bond 0.00448 ( 58) link_NAG-ASN : angle 2.82572 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 346 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7207 (mt0) REVERT: E 69 TRP cc_start: 0.7648 (m-90) cc_final: 0.7371 (m-90) REVERT: E 72 HIS cc_start: 0.5446 (p90) cc_final: 0.5176 (p-80) REVERT: F 161 MET cc_start: 0.7907 (tpp) cc_final: 0.7669 (tpp) REVERT: F 195 ASN cc_start: 0.7537 (m-40) cc_final: 0.7258 (m110) REVERT: F 475 MET cc_start: 0.8838 (tpp) cc_final: 0.8620 (tpp) REVERT: J 3 GLN cc_start: 0.7801 (mt0) cc_final: 0.7564 (mp10) REVERT: J 78 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7696 (m-80) REVERT: M 91 TYR cc_start: 0.6631 (m-80) cc_final: 0.6409 (m-10) REVERT: Q 10 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7298 (tm-30) REVERT: S 86 ASP cc_start: 0.8277 (m-30) cc_final: 0.7992 (m-30) REVERT: T 27 GLN cc_start: 0.8287 (mt0) cc_final: 0.7920 (pt0) REVERT: T 70 ASP cc_start: 0.7587 (m-30) cc_final: 0.6808 (p0) REVERT: I 33 PHE cc_start: 0.6886 (m-80) cc_final: 0.6636 (m-80) REVERT: I 49 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6701 (m-30) REVERT: I 102 ARG cc_start: 0.7027 (mmm-85) cc_final: 0.6734 (mmm-85) REVERT: L 20 ILE cc_start: 0.7700 (mm) cc_final: 0.7408 (mm) REVERT: L 61 PHE cc_start: 0.6605 (m-80) cc_final: 0.6264 (m-80) REVERT: N 18 VAL cc_start: 0.6841 (p) cc_final: 0.6517 (t) outliers start: 33 outliers final: 21 residues processed: 365 average time/residue: 0.1617 time to fit residues: 94.6922 Evaluate side-chains 336 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 312 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 101 GLU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 23 CYS Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 chunk 253 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 293 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN B 652 GLN E 195 ASN E 428 GLN ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.147355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118037 restraints weight = 40033.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117398 restraints weight = 30413.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.118752 restraints weight = 26499.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119246 restraints weight = 19931.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119477 restraints weight = 18390.595| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26188 Z= 0.114 Angle : 0.718 12.468 35849 Z= 0.348 Chirality : 0.048 0.301 4363 Planarity : 0.004 0.063 4300 Dihedral : 12.111 106.392 5982 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.09 % Favored : 92.61 % Rotamer: Outliers : 1.77 % Allowed : 11.26 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.15), residues: 2991 helix: -2.59 (0.24), residues: 348 sheet: -0.87 (0.18), residues: 933 loop : -2.04 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 66 TYR 0.023 0.001 TYR M 52 PHE 0.010 0.001 PHE I 61 TRP 0.024 0.001 TRP M 47 HIS 0.003 0.001 HIS O 100F Details of bonding type rmsd covalent geometry : bond 0.00239 (26009) covalent geometry : angle 0.68230 (35357) SS BOND : bond 0.00411 ( 45) SS BOND : angle 1.40257 ( 90) hydrogen bonds : bond 0.03928 ( 567) hydrogen bonds : angle 5.63110 ( 1500) link_ALPHA1-2 : bond 0.00580 ( 9) link_ALPHA1-2 : angle 1.80270 ( 27) link_ALPHA1-3 : bond 0.00963 ( 14) link_ALPHA1-3 : angle 1.59071 ( 42) link_ALPHA1-6 : bond 0.00729 ( 12) link_ALPHA1-6 : angle 1.99983 ( 36) link_BETA1-4 : bond 0.00518 ( 39) link_BETA1-4 : angle 1.85515 ( 117) link_BETA1-6 : bond 0.00431 ( 2) link_BETA1-6 : angle 1.27999 ( 6) link_NAG-ASN : bond 0.00401 ( 58) link_NAG-ASN : angle 2.51509 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 332 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7242 (mt0) REVERT: B 626 MET cc_start: 0.9214 (mtt) cc_final: 0.8644 (mtt) REVERT: E 72 HIS cc_start: 0.5249 (p90) cc_final: 0.4968 (p-80) REVERT: F 99 ASN cc_start: 0.8511 (t0) cc_final: 0.8147 (t0) REVERT: G 128 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8741 (m) REVERT: H 53 ASN cc_start: 0.6321 (p0) cc_final: 0.6053 (p0) REVERT: J 78 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: M 31 SER cc_start: 0.8463 (m) cc_final: 0.8118 (m) REVERT: M 53 ASN cc_start: 0.7064 (p0) cc_final: 0.6543 (t0) REVERT: P 102 THR cc_start: 0.8846 (p) cc_final: 0.8471 (t) REVERT: Q 10 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7499 (tm-30) REVERT: Q 86 ASP cc_start: 0.7974 (m-30) cc_final: 0.7657 (m-30) REVERT: T 27 GLN cc_start: 0.8257 (mt0) cc_final: 0.7884 (pt0) REVERT: T 70 ASP cc_start: 0.7533 (m-30) cc_final: 0.6857 (p0) REVERT: I 49 ASP cc_start: 0.6806 (OUTLIER) cc_final: 0.6579 (m-30) REVERT: L 20 ILE cc_start: 0.7846 (mm) cc_final: 0.7545 (mm) REVERT: L 41 MET cc_start: 0.7426 (mmm) cc_final: 0.6937 (ttm) REVERT: L 61 PHE cc_start: 0.6548 (m-80) cc_final: 0.6273 (m-80) REVERT: L 86 TYR cc_start: 0.7046 (m-80) cc_final: 0.6743 (m-80) REVERT: N 18 VAL cc_start: 0.6798 (p) cc_final: 0.6582 (m) outliers start: 46 outliers final: 28 residues processed: 364 average time/residue: 0.1593 time to fit residues: 93.3241 Evaluate side-chains 328 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 296 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain N residue 74 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 9.9990 chunk 282 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 136 optimal weight: 0.3980 chunk 272 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 GLN E 195 ASN E 428 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 HIS S 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116211 restraints weight = 39847.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115251 restraints weight = 29471.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116515 restraints weight = 27569.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117030 restraints weight = 20549.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117310 restraints weight = 18793.747| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26188 Z= 0.151 Angle : 0.730 12.217 35849 Z= 0.354 Chirality : 0.049 0.299 4363 Planarity : 0.004 0.062 4300 Dihedral : 11.356 105.550 5982 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.46 % Favored : 92.21 % Rotamer: Outliers : 2.38 % Allowed : 13.65 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.15), residues: 2991 helix: -2.42 (0.24), residues: 369 sheet: -0.95 (0.17), residues: 963 loop : -1.97 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 102 TYR 0.025 0.001 TYR M 52 PHE 0.012 0.001 PHE F 53 TRP 0.016 0.001 TRP M 47 HIS 0.004 0.001 HIS O 100F Details of bonding type rmsd covalent geometry : bond 0.00349 (26009) covalent geometry : angle 0.69435 (35357) SS BOND : bond 0.00532 ( 45) SS BOND : angle 1.60716 ( 90) hydrogen bonds : bond 0.03883 ( 567) hydrogen bonds : angle 5.36062 ( 1500) link_ALPHA1-2 : bond 0.00496 ( 9) link_ALPHA1-2 : angle 1.91447 ( 27) link_ALPHA1-3 : bond 0.00918 ( 14) link_ALPHA1-3 : angle 1.69579 ( 42) link_ALPHA1-6 : bond 0.00646 ( 12) link_ALPHA1-6 : angle 1.99392 ( 36) link_BETA1-4 : bond 0.00512 ( 39) link_BETA1-4 : angle 1.87009 ( 117) link_BETA1-6 : bond 0.00425 ( 2) link_BETA1-6 : angle 1.23388 ( 6) link_NAG-ASN : bond 0.00357 ( 58) link_NAG-ASN : angle 2.44585 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 309 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7231 (mt0) REVERT: B 626 MET cc_start: 0.9194 (mtt) cc_final: 0.8657 (mtt) REVERT: F 95 MET cc_start: 0.8286 (ptm) cc_final: 0.8028 (ptt) REVERT: F 475 MET cc_start: 0.8857 (tpp) cc_final: 0.8559 (tpp) REVERT: H 53 ASN cc_start: 0.6531 (p0) cc_final: 0.6291 (p0) REVERT: J 78 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: J 111 VAL cc_start: 0.6018 (OUTLIER) cc_final: 0.5702 (m) REVERT: M 27 TYR cc_start: 0.8281 (t80) cc_final: 0.8051 (t80) REVERT: M 31 SER cc_start: 0.8529 (m) cc_final: 0.8177 (m) REVERT: M 53 ASN cc_start: 0.7149 (p0) cc_final: 0.6635 (t0) REVERT: M 91 TYR cc_start: 0.6622 (m-80) cc_final: 0.6404 (m-10) REVERT: P 102 THR cc_start: 0.8876 (p) cc_final: 0.8466 (t) REVERT: Q 10 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7478 (tm-30) REVERT: Q 11 VAL cc_start: 0.7260 (OUTLIER) cc_final: 0.6698 (t) REVERT: T 27 GLN cc_start: 0.8229 (mt0) cc_final: 0.7848 (pt0) REVERT: T 70 ASP cc_start: 0.7511 (m-30) cc_final: 0.6805 (p0) REVERT: L 20 ILE cc_start: 0.7854 (mm) cc_final: 0.7534 (mm) REVERT: L 41 MET cc_start: 0.7272 (mmm) cc_final: 0.6791 (ttm) REVERT: L 61 PHE cc_start: 0.6546 (m-80) cc_final: 0.6250 (m-80) REVERT: N 18 VAL cc_start: 0.6886 (p) cc_final: 0.6638 (m) REVERT: N 19 THR cc_start: 0.6445 (p) cc_final: 0.6158 (p) outliers start: 62 outliers final: 41 residues processed: 353 average time/residue: 0.1559 time to fit residues: 89.3841 Evaluate side-chains 340 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 74 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 145 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 252 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 282 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 235 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 GLN E 66 HIS E 195 ASN E 428 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113244 restraints weight = 39882.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.112267 restraints weight = 30046.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113471 restraints weight = 28388.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.113992 restraints weight = 20942.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114275 restraints weight = 19215.658| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 26188 Z= 0.233 Angle : 0.801 11.760 35849 Z= 0.390 Chirality : 0.051 0.283 4363 Planarity : 0.004 0.056 4300 Dihedral : 11.288 105.625 5982 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.39 % Favored : 90.30 % Rotamer: Outliers : 3.00 % Allowed : 14.03 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.15), residues: 2991 helix: -2.47 (0.24), residues: 372 sheet: -0.90 (0.17), residues: 945 loop : -2.07 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 617 TYR 0.029 0.002 TYR M 52 PHE 0.019 0.002 PHE F 53 TRP 0.013 0.001 TRP F 96 HIS 0.006 0.001 HIS M 98 Details of bonding type rmsd covalent geometry : bond 0.00563 (26009) covalent geometry : angle 0.76441 (35357) SS BOND : bond 0.00639 ( 45) SS BOND : angle 1.92292 ( 90) hydrogen bonds : bond 0.04340 ( 567) hydrogen bonds : angle 5.33173 ( 1500) link_ALPHA1-2 : bond 0.00454 ( 9) link_ALPHA1-2 : angle 2.08462 ( 27) link_ALPHA1-3 : bond 0.00858 ( 14) link_ALPHA1-3 : angle 1.76821 ( 42) link_ALPHA1-6 : bond 0.00549 ( 12) link_ALPHA1-6 : angle 2.04809 ( 36) link_BETA1-4 : bond 0.00537 ( 39) link_BETA1-4 : angle 2.01666 ( 117) link_BETA1-6 : bond 0.00466 ( 2) link_BETA1-6 : angle 1.21864 ( 6) link_NAG-ASN : bond 0.00378 ( 58) link_NAG-ASN : angle 2.54317 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 287 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7226 (mt0) REVERT: B 626 MET cc_start: 0.9258 (mtt) cc_final: 0.8740 (mtt) REVERT: E 66 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.7012 (m-70) REVERT: F 161 MET cc_start: 0.7846 (tpp) cc_final: 0.7562 (tpp) REVERT: F 475 MET cc_start: 0.8983 (tpp) cc_final: 0.8627 (tpp) REVERT: G 195 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7542 (t0) REVERT: H 53 ASN cc_start: 0.7091 (p0) cc_final: 0.6781 (p0) REVERT: J 53 ASN cc_start: 0.7973 (p0) cc_final: 0.7654 (p0) REVERT: J 71 GLN cc_start: 0.8275 (pp30) cc_final: 0.7826 (pp30) REVERT: J 78 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: J 111 VAL cc_start: 0.6115 (OUTLIER) cc_final: 0.5741 (m) REVERT: M 6 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7166 (tm-30) REVERT: M 91 TYR cc_start: 0.6645 (m-80) cc_final: 0.6373 (m-10) REVERT: P 102 THR cc_start: 0.8888 (p) cc_final: 0.8469 (t) REVERT: Q 10 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7501 (tm-30) REVERT: Q 11 VAL cc_start: 0.7202 (OUTLIER) cc_final: 0.6729 (t) REVERT: T 27 GLN cc_start: 0.8270 (mt0) cc_final: 0.7885 (pt0) REVERT: T 70 ASP cc_start: 0.7606 (m-30) cc_final: 0.6952 (p0) REVERT: L 20 ILE cc_start: 0.7850 (mm) cc_final: 0.7533 (mm) REVERT: L 41 MET cc_start: 0.7265 (mmm) cc_final: 0.6837 (ttm) REVERT: L 61 PHE cc_start: 0.6557 (m-80) cc_final: 0.6091 (m-80) REVERT: L 86 TYR cc_start: 0.7091 (m-80) cc_final: 0.6845 (m-80) REVERT: N 18 VAL cc_start: 0.6933 (p) cc_final: 0.6646 (m) REVERT: N 19 THR cc_start: 0.6400 (OUTLIER) cc_final: 0.6127 (p) REVERT: N 60 ARG cc_start: 0.7487 (mtm110) cc_final: 0.7285 (ttp-110) outliers start: 78 outliers final: 55 residues processed: 342 average time/residue: 0.1563 time to fit residues: 86.5632 Evaluate side-chains 340 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 278 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 74 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 176 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 GLN E 66 HIS E 195 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.115176 restraints weight = 39985.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114309 restraints weight = 30129.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115605 restraints weight = 27253.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116098 restraints weight = 20278.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116358 restraints weight = 18736.601| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26188 Z= 0.148 Angle : 0.732 11.854 35849 Z= 0.356 Chirality : 0.049 0.288 4363 Planarity : 0.004 0.060 4300 Dihedral : 10.749 104.953 5982 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.56 % Favored : 92.14 % Rotamer: Outliers : 3.11 % Allowed : 15.42 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.15), residues: 2991 helix: -2.08 (0.25), residues: 351 sheet: -0.78 (0.17), residues: 933 loop : -1.99 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 617 TYR 0.026 0.001 TYR M 52 PHE 0.012 0.001 PHE S 91 TRP 0.012 0.001 TRP M 47 HIS 0.018 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00341 (26009) covalent geometry : angle 0.69687 (35357) SS BOND : bond 0.00535 ( 45) SS BOND : angle 1.64290 ( 90) hydrogen bonds : bond 0.03755 ( 567) hydrogen bonds : angle 5.16045 ( 1500) link_ALPHA1-2 : bond 0.00537 ( 9) link_ALPHA1-2 : angle 1.93312 ( 27) link_ALPHA1-3 : bond 0.00914 ( 14) link_ALPHA1-3 : angle 1.66359 ( 42) link_ALPHA1-6 : bond 0.00675 ( 12) link_ALPHA1-6 : angle 1.86689 ( 36) link_BETA1-4 : bond 0.00491 ( 39) link_BETA1-4 : angle 1.83349 ( 117) link_BETA1-6 : bond 0.00431 ( 2) link_BETA1-6 : angle 1.21522 ( 6) link_NAG-ASN : bond 0.00354 ( 58) link_NAG-ASN : angle 2.45672 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 288 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7239 (mt0) REVERT: B 626 MET cc_start: 0.9209 (mtt) cc_final: 0.8704 (mtt) REVERT: E 66 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6901 (m-70) REVERT: E 275 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: F 161 MET cc_start: 0.7771 (tpp) cc_final: 0.6547 (tpt) REVERT: F 475 MET cc_start: 0.8978 (tpp) cc_final: 0.8604 (tpp) REVERT: G 95 MET cc_start: 0.8670 (ptm) cc_final: 0.8079 (ttp) REVERT: G 195 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7440 (t0) REVERT: H 53 ASN cc_start: 0.6846 (p0) cc_final: 0.6555 (p0) REVERT: J 71 GLN cc_start: 0.8244 (pp30) cc_final: 0.7989 (pp30) REVERT: J 111 VAL cc_start: 0.6008 (OUTLIER) cc_final: 0.5641 (m) REVERT: M 6 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6965 (tm-30) REVERT: O 87 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8309 (t) REVERT: P 102 THR cc_start: 0.8886 (p) cc_final: 0.8460 (t) REVERT: Q 10 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7516 (tm-30) REVERT: Q 11 VAL cc_start: 0.7246 (OUTLIER) cc_final: 0.6789 (t) REVERT: T 27 GLN cc_start: 0.8278 (mt0) cc_final: 0.7911 (pt0) REVERT: T 70 ASP cc_start: 0.7539 (m-30) cc_final: 0.6909 (p0) REVERT: L 20 ILE cc_start: 0.7808 (mm) cc_final: 0.7479 (mm) REVERT: L 41 MET cc_start: 0.7250 (mmm) cc_final: 0.6840 (ttm) REVERT: L 61 PHE cc_start: 0.6480 (m-80) cc_final: 0.6052 (m-80) REVERT: L 86 TYR cc_start: 0.7031 (m-80) cc_final: 0.6797 (m-80) REVERT: N 18 VAL cc_start: 0.6906 (p) cc_final: 0.6651 (m) REVERT: N 19 THR cc_start: 0.6458 (OUTLIER) cc_final: 0.6179 (p) outliers start: 81 outliers final: 59 residues processed: 350 average time/residue: 0.1533 time to fit residues: 86.8795 Evaluate side-chains 349 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 282 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 74 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 166 optimal weight: 0.4980 chunk 177 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 54 optimal weight: 0.0980 chunk 114 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 163 optimal weight: 0.0060 chunk 188 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS E 72 HIS E 195 ASN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.147917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118423 restraints weight = 39668.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117999 restraints weight = 30074.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119266 restraints weight = 25958.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119832 restraints weight = 19872.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120086 restraints weight = 18461.023| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26188 Z= 0.108 Angle : 0.686 12.029 35849 Z= 0.333 Chirality : 0.047 0.295 4363 Planarity : 0.004 0.061 4300 Dihedral : 9.980 102.746 5982 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.79 % Favored : 92.98 % Rotamer: Outliers : 2.73 % Allowed : 15.92 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.15), residues: 2991 helix: -1.64 (0.27), residues: 351 sheet: -0.73 (0.17), residues: 921 loop : -1.81 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 48 TYR 0.019 0.001 TYR M 52 PHE 0.016 0.001 PHE I 61 TRP 0.012 0.001 TRP M 47 HIS 0.026 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00224 (26009) covalent geometry : angle 0.65255 (35357) SS BOND : bond 0.00503 ( 45) SS BOND : angle 1.61631 ( 90) hydrogen bonds : bond 0.03158 ( 567) hydrogen bonds : angle 4.90094 ( 1500) link_ALPHA1-2 : bond 0.00657 ( 9) link_ALPHA1-2 : angle 1.83696 ( 27) link_ALPHA1-3 : bond 0.00935 ( 14) link_ALPHA1-3 : angle 1.57424 ( 42) link_ALPHA1-6 : bond 0.00825 ( 12) link_ALPHA1-6 : angle 1.68766 ( 36) link_BETA1-4 : bond 0.00496 ( 39) link_BETA1-4 : angle 1.64873 ( 117) link_BETA1-6 : bond 0.00422 ( 2) link_BETA1-6 : angle 1.24459 ( 6) link_NAG-ASN : bond 0.00377 ( 58) link_NAG-ASN : angle 2.33328 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 304 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7214 (mt0) REVERT: B 626 MET cc_start: 0.9183 (mtt) cc_final: 0.8713 (mtt) REVERT: E 66 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6809 (m-70) REVERT: E 275 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: F 99 ASN cc_start: 0.8526 (t0) cc_final: 0.8157 (t0) REVERT: F 161 MET cc_start: 0.7611 (tpp) cc_final: 0.6552 (tpt) REVERT: F 475 MET cc_start: 0.8958 (tpp) cc_final: 0.8665 (tpp) REVERT: G 95 MET cc_start: 0.8625 (ptm) cc_final: 0.8049 (ttp) REVERT: G 195 ASN cc_start: 0.7667 (OUTLIER) cc_final: 0.7448 (t0) REVERT: H 91 TYR cc_start: 0.7760 (m-80) cc_final: 0.7156 (m-80) REVERT: J 3 GLN cc_start: 0.7817 (mp10) cc_final: 0.7228 (mp10) REVERT: J 53 ASN cc_start: 0.7561 (p0) cc_final: 0.7016 (t0) REVERT: J 111 VAL cc_start: 0.5944 (OUTLIER) cc_final: 0.5591 (m) REVERT: M 6 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6963 (tm-30) REVERT: P 102 THR cc_start: 0.8843 (p) cc_final: 0.8453 (t) REVERT: Q 10 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7505 (tm-30) REVERT: Q 11 VAL cc_start: 0.7309 (OUTLIER) cc_final: 0.6872 (t) REVERT: Q 68 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8279 (tt) REVERT: S 77 ILE cc_start: 0.9030 (tt) cc_final: 0.8712 (tp) REVERT: T 27 GLN cc_start: 0.8252 (mt0) cc_final: 0.7897 (pt0) REVERT: T 70 ASP cc_start: 0.7382 (m-30) cc_final: 0.6921 (p0) REVERT: L 20 ILE cc_start: 0.7807 (mm) cc_final: 0.7497 (mm) REVERT: L 41 MET cc_start: 0.7187 (mmm) cc_final: 0.6772 (ttm) REVERT: L 61 PHE cc_start: 0.6430 (m-80) cc_final: 0.6182 (m-80) REVERT: N 18 VAL cc_start: 0.6857 (p) cc_final: 0.6616 (m) REVERT: N 19 THR cc_start: 0.6450 (OUTLIER) cc_final: 0.6174 (p) outliers start: 71 outliers final: 51 residues processed: 353 average time/residue: 0.1545 time to fit residues: 87.7043 Evaluate side-chains 345 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 286 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 103 optimal weight: 8.9990 chunk 271 optimal weight: 0.8980 chunk 199 optimal weight: 0.8980 chunk 197 optimal weight: 0.0050 chunk 108 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 86 optimal weight: 0.0570 chunk 123 optimal weight: 3.9990 chunk 287 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 overall best weight: 1.1714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS E 72 HIS E 195 ASN E 428 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN S 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117578 restraints weight = 39545.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116902 restraints weight = 29939.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118158 restraints weight = 26695.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118653 restraints weight = 20097.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118894 restraints weight = 18568.843| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26188 Z= 0.119 Angle : 0.688 11.942 35849 Z= 0.333 Chirality : 0.047 0.293 4363 Planarity : 0.004 0.057 4300 Dihedral : 9.655 100.823 5982 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.42 % Favored : 92.34 % Rotamer: Outliers : 2.69 % Allowed : 16.42 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.15), residues: 2991 helix: -1.42 (0.27), residues: 351 sheet: -0.60 (0.17), residues: 939 loop : -1.80 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 24 TYR 0.018 0.001 TYR M 52 PHE 0.014 0.001 PHE I 61 TRP 0.009 0.001 TRP M 47 HIS 0.013 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00263 (26009) covalent geometry : angle 0.65512 (35357) SS BOND : bond 0.00501 ( 45) SS BOND : angle 1.74306 ( 90) hydrogen bonds : bond 0.03208 ( 567) hydrogen bonds : angle 4.79214 ( 1500) link_ALPHA1-2 : bond 0.00702 ( 9) link_ALPHA1-2 : angle 1.88025 ( 27) link_ALPHA1-3 : bond 0.00898 ( 14) link_ALPHA1-3 : angle 1.63250 ( 42) link_ALPHA1-6 : bond 0.00785 ( 12) link_ALPHA1-6 : angle 1.68857 ( 36) link_BETA1-4 : bond 0.00484 ( 39) link_BETA1-4 : angle 1.66087 ( 117) link_BETA1-6 : bond 0.00409 ( 2) link_BETA1-6 : angle 1.21496 ( 6) link_NAG-ASN : bond 0.00347 ( 58) link_NAG-ASN : angle 2.27581 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 288 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7218 (mt0) REVERT: B 626 MET cc_start: 0.9196 (mtt) cc_final: 0.8731 (mtt) REVERT: E 275 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: F 99 ASN cc_start: 0.8564 (t0) cc_final: 0.8188 (t0) REVERT: F 161 MET cc_start: 0.7678 (tpp) cc_final: 0.6531 (tpt) REVERT: F 475 MET cc_start: 0.8954 (tpp) cc_final: 0.8594 (tpp) REVERT: G 95 MET cc_start: 0.8635 (ptm) cc_final: 0.8088 (ttp) REVERT: G 195 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7352 (t0) REVERT: J 53 ASN cc_start: 0.7471 (p0) cc_final: 0.6895 (t0) REVERT: J 111 VAL cc_start: 0.5845 (OUTLIER) cc_final: 0.5499 (m) REVERT: P 102 THR cc_start: 0.8852 (p) cc_final: 0.8433 (t) REVERT: Q 10 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7494 (tm-30) REVERT: Q 11 VAL cc_start: 0.7347 (OUTLIER) cc_final: 0.7129 (t) REVERT: Q 68 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8307 (tt) REVERT: R 77 ASN cc_start: 0.7474 (t0) cc_final: 0.7257 (t0) REVERT: S 77 ILE cc_start: 0.9040 (tt) cc_final: 0.8726 (tp) REVERT: T 27 GLN cc_start: 0.8296 (mt0) cc_final: 0.7922 (pt0) REVERT: T 70 ASP cc_start: 0.7377 (m-30) cc_final: 0.6986 (p0) REVERT: L 20 ILE cc_start: 0.7875 (mm) cc_final: 0.7595 (mm) REVERT: L 41 MET cc_start: 0.7186 (mmm) cc_final: 0.6818 (ttm) REVERT: L 61 PHE cc_start: 0.6450 (m-80) cc_final: 0.6153 (m-80) REVERT: N 18 VAL cc_start: 0.6848 (p) cc_final: 0.6618 (m) REVERT: N 19 THR cc_start: 0.6436 (OUTLIER) cc_final: 0.6183 (p) outliers start: 70 outliers final: 52 residues processed: 340 average time/residue: 0.1563 time to fit residues: 85.7423 Evaluate side-chains 337 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 278 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 279 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 175 optimal weight: 0.0010 chunk 199 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 216 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 HIS E 195 ASN E 428 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 GLN L 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.148903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119635 restraints weight = 39687.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119072 restraints weight = 28826.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.120248 restraints weight = 26644.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120745 restraints weight = 20082.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.120998 restraints weight = 18469.255| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26188 Z= 0.108 Angle : 0.669 11.966 35849 Z= 0.324 Chirality : 0.046 0.282 4363 Planarity : 0.003 0.058 4300 Dihedral : 9.205 98.620 5982 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.09 % Favored : 92.71 % Rotamer: Outliers : 2.50 % Allowed : 16.80 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.15), residues: 2991 helix: -1.14 (0.28), residues: 351 sheet: -0.45 (0.18), residues: 924 loop : -1.70 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 24 TYR 0.015 0.001 TYR J 91 PHE 0.017 0.001 PHE I 61 TRP 0.010 0.001 TRP M 47 HIS 0.002 0.001 HIS O 100F Details of bonding type rmsd covalent geometry : bond 0.00231 (26009) covalent geometry : angle 0.63776 (35357) SS BOND : bond 0.00450 ( 45) SS BOND : angle 1.53668 ( 90) hydrogen bonds : bond 0.03024 ( 567) hydrogen bonds : angle 4.67009 ( 1500) link_ALPHA1-2 : bond 0.00758 ( 9) link_ALPHA1-2 : angle 1.77324 ( 27) link_ALPHA1-3 : bond 0.00890 ( 14) link_ALPHA1-3 : angle 1.58117 ( 42) link_ALPHA1-6 : bond 0.00824 ( 12) link_ALPHA1-6 : angle 1.65637 ( 36) link_BETA1-4 : bond 0.00490 ( 39) link_BETA1-4 : angle 1.61263 ( 117) link_BETA1-6 : bond 0.00413 ( 2) link_BETA1-6 : angle 1.22106 ( 6) link_NAG-ASN : bond 0.00344 ( 58) link_NAG-ASN : angle 2.20736 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 302 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7176 (mt0) REVERT: A 654 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7473 (mt-10) REVERT: E 275 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: F 99 ASN cc_start: 0.8550 (t0) cc_final: 0.8182 (t0) REVERT: F 161 MET cc_start: 0.7604 (tpp) cc_final: 0.7162 (mmm) REVERT: F 475 MET cc_start: 0.8937 (tpp) cc_final: 0.8559 (tpp) REVERT: G 95 MET cc_start: 0.8692 (ptm) cc_final: 0.8081 (ttp) REVERT: G 161 MET cc_start: 0.6865 (ttm) cc_final: 0.6593 (ttt) REVERT: G 195 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.7214 (t0) REVERT: J 3 GLN cc_start: 0.7908 (mp10) cc_final: 0.7305 (mp10) REVERT: J 53 ASN cc_start: 0.7398 (p0) cc_final: 0.6886 (t0) REVERT: P 102 THR cc_start: 0.8906 (p) cc_final: 0.8469 (t) REVERT: Q 10 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7478 (tm-30) REVERT: Q 11 VAL cc_start: 0.7325 (OUTLIER) cc_final: 0.7121 (t) REVERT: Q 68 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8265 (tt) REVERT: R 77 ASN cc_start: 0.7409 (t0) cc_final: 0.7164 (t0) REVERT: S 77 ILE cc_start: 0.9019 (tt) cc_final: 0.8705 (tp) REVERT: T 27 GLN cc_start: 0.8299 (mt0) cc_final: 0.7928 (pt0) REVERT: T 70 ASP cc_start: 0.7332 (m-30) cc_final: 0.6960 (p0) REVERT: L 36 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.6433 (pp30) REVERT: L 41 MET cc_start: 0.7197 (mmm) cc_final: 0.6890 (ttm) REVERT: L 61 PHE cc_start: 0.6414 (m-80) cc_final: 0.6133 (m-80) REVERT: N 18 VAL cc_start: 0.6839 (p) cc_final: 0.6597 (m) REVERT: N 19 THR cc_start: 0.6397 (OUTLIER) cc_final: 0.6120 (p) outliers start: 65 outliers final: 49 residues processed: 351 average time/residue: 0.1582 time to fit residues: 89.5546 Evaluate side-chains 344 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 288 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 151 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 213 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 261 optimal weight: 0.0770 chunk 94 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120098 restraints weight = 39656.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119727 restraints weight = 29177.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120896 restraints weight = 25928.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121438 restraints weight = 19866.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121655 restraints weight = 18203.973| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26188 Z= 0.107 Angle : 0.665 12.054 35849 Z= 0.322 Chirality : 0.046 0.270 4363 Planarity : 0.003 0.056 4300 Dihedral : 8.961 96.939 5982 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.02 % Favored : 92.78 % Rotamer: Outliers : 2.00 % Allowed : 17.53 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.15), residues: 2991 helix: -0.96 (0.28), residues: 351 sheet: -0.38 (0.18), residues: 924 loop : -1.64 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 20 TYR 0.014 0.001 TYR M 52 PHE 0.019 0.001 PHE L 38 TRP 0.015 0.001 TRP H 35 HIS 0.002 0.001 HIS O 100E Details of bonding type rmsd covalent geometry : bond 0.00230 (26009) covalent geometry : angle 0.63428 (35357) SS BOND : bond 0.00435 ( 45) SS BOND : angle 1.52779 ( 90) hydrogen bonds : bond 0.02985 ( 567) hydrogen bonds : angle 4.59630 ( 1500) link_ALPHA1-2 : bond 0.00748 ( 9) link_ALPHA1-2 : angle 1.74084 ( 27) link_ALPHA1-3 : bond 0.00876 ( 14) link_ALPHA1-3 : angle 1.55988 ( 42) link_ALPHA1-6 : bond 0.00789 ( 12) link_ALPHA1-6 : angle 1.65324 ( 36) link_BETA1-4 : bond 0.00489 ( 39) link_BETA1-4 : angle 1.59809 ( 117) link_BETA1-6 : bond 0.00410 ( 2) link_BETA1-6 : angle 1.21964 ( 6) link_NAG-ASN : bond 0.00339 ( 58) link_NAG-ASN : angle 2.17026 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 300 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7197 (mt0) REVERT: A 654 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7500 (mt-10) REVERT: B 626 MET cc_start: 0.9000 (mtt) cc_final: 0.8707 (mtt) REVERT: C 625 ASN cc_start: 0.8291 (t0) cc_final: 0.7818 (t0) REVERT: E 275 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: F 99 ASN cc_start: 0.8529 (t0) cc_final: 0.8174 (t0) REVERT: F 475 MET cc_start: 0.8936 (tpp) cc_final: 0.8548 (tpp) REVERT: G 95 MET cc_start: 0.8691 (ptm) cc_final: 0.8016 (ttp) REVERT: G 161 MET cc_start: 0.6804 (ttm) cc_final: 0.6535 (ttt) REVERT: G 195 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.7210 (t0) REVERT: H 91 TYR cc_start: 0.7718 (m-80) cc_final: 0.7111 (m-80) REVERT: J 3 GLN cc_start: 0.7888 (mp10) cc_final: 0.7280 (mp10) REVERT: J 53 ASN cc_start: 0.7280 (p0) cc_final: 0.6843 (t0) REVERT: J 111 VAL cc_start: 0.5772 (OUTLIER) cc_final: 0.5442 (m) REVERT: P 102 THR cc_start: 0.8877 (p) cc_final: 0.8435 (t) REVERT: Q 10 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7442 (tm-30) REVERT: Q 68 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8281 (tt) REVERT: R 77 ASN cc_start: 0.7370 (t0) cc_final: 0.7116 (t0) REVERT: S 77 ILE cc_start: 0.9017 (tt) cc_final: 0.8695 (tp) REVERT: T 27 GLN cc_start: 0.8291 (mt0) cc_final: 0.7927 (pt0) REVERT: T 70 ASP cc_start: 0.7261 (m-30) cc_final: 0.6934 (p0) REVERT: L 41 MET cc_start: 0.7069 (mmm) cc_final: 0.6714 (ttm) REVERT: L 61 PHE cc_start: 0.6406 (m-80) cc_final: 0.6129 (m-80) REVERT: N 18 VAL cc_start: 0.6711 (p) cc_final: 0.6509 (m) REVERT: N 19 THR cc_start: 0.6412 (OUTLIER) cc_final: 0.6133 (p) outliers start: 52 outliers final: 42 residues processed: 339 average time/residue: 0.1544 time to fit residues: 83.9742 Evaluate side-chains 342 residues out of total 2646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 294 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 78 PHE Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 102 SER Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 199 optimal weight: 0.0980 chunk 164 optimal weight: 0.0070 chunk 133 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 131 optimal weight: 0.2980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 440 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 = 0.3816 r_free = 0.3816 target = 0.150801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121314 restraints weight = 39368.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121119 restraints weight = 29728.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122334 restraints weight = 25683.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122953 restraints weight = 19833.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123512 restraints weight = 18370.705| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26188 Z= 0.103 Angle : 0.651 11.941 35849 Z= 0.315 Chirality : 0.046 0.257 4363 Planarity : 0.003 0.057 4300 Dihedral : 8.524 93.051 5982 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.02 % Favored : 92.81 % Rotamer: Outliers : 1.88 % Allowed : 17.84 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.15), residues: 2991 helix: -0.76 (0.29), residues: 357 sheet: -0.28 (0.18), residues: 915 loop : -1.59 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 66 TYR 0.014 0.001 TYR F 484 PHE 0.016 0.001 PHE I 61 TRP 0.011 0.001 TRP H 35 HIS 0.002 0.001 HIS Q 3 Details of bonding type rmsd covalent geometry : bond 0.00220 (26009) covalent geometry : angle 0.62121 (35357) SS BOND : bond 0.00402 ( 45) SS BOND : angle 1.39881 ( 90) hydrogen bonds : bond 0.02856 ( 567) hydrogen bonds : angle 4.44844 ( 1500) link_ALPHA1-2 : bond 0.00742 ( 9) link_ALPHA1-2 : angle 1.71252 ( 27) link_ALPHA1-3 : bond 0.00852 ( 14) link_ALPHA1-3 : angle 1.53488 ( 42) link_ALPHA1-6 : bond 0.00782 ( 12) link_ALPHA1-6 : angle 1.75097 ( 36) link_BETA1-4 : bond 0.00492 ( 39) link_BETA1-4 : angle 1.57168 ( 117) link_BETA1-6 : bond 0.00403 ( 2) link_BETA1-6 : angle 1.22011 ( 6) link_NAG-ASN : bond 0.00335 ( 58) link_NAG-ASN : angle 2.09405 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3823.83 seconds wall clock time: 67 minutes 4.42 seconds (4024.42 seconds total)