Starting phenix.real_space_refine on Wed Nov 19 01:44:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dcq_7858/11_2025/6dcq_7858.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dcq_7858/11_2025/6dcq_7858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dcq_7858/11_2025/6dcq_7858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dcq_7858/11_2025/6dcq_7858.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dcq_7858/11_2025/6dcq_7858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dcq_7858/11_2025/6dcq_7858.map" } resolution = 3.1 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= 0.008 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 110 5.16 5 C 12064 2.51 5 N 3154 2.21 5 O 3972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19300 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 3413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 435, 3403 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 435, 3403 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 5 bond proxies already assigned to first conformer: 3458 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3538 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 452, 3538 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 23, 'TRANS': 428} Chain breaks: 4 bond proxies already assigned to first conformer: 3592 Chain: "D" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1167 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 1, 'TRANS': 144} Chain: "E" Number of atoms: 3536 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 448, 3515 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 23, 'TRANS': 424} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 448, 3515 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 23, 'TRANS': 424} Chain breaks: 4 bond proxies already assigned to first conformer: 3563 Chain: "F" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1095 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "H" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1050 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "L" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "M" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1067 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} 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: "g" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 113 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 5} 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 113 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 5} 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: "s" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 110 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 1, 'NAG': 4} 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: 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 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS A 173 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 173 " occ=0.50 residue: pdb=" N AHIS E 173 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 173 " occ=0.50 residue: pdb=" N AARG E 444 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 444 " occ=0.50 Time building chain proxies: 6.49, per 1000 atoms: 0.34 Number of scatterers: 19300 At special positions: 0 Unit cell: (152.44, 133.9, 128.75, 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 110 16.00 O 3972 8.00 N 3154 7.00 C 12064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.23 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN k 4 " - " MAN k 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 9 " " BMA g 3 " - " MAN g 4 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA c 3 " - " MAN c 5 " " BMA f 3 " - " MAN f 4 " " BMA g 3 " - " MAN g 7 " " BMA k 3 " - " MAN k 6 " " BMA r 3 " - " MAN r 7 " " BMA s 3 " - " MAN s 4 " BETA1-2 " MAN f 4 " - " NAG f 5 " " MAN g 4 " - " NAG g 5 " " MAN g 7 " - " NAG g 8 " " MAN r 4 " - " NAG r 5 " " MAN r 7 " - " NAG r 8 " " MAN s 4 " - " NAG s 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG f 5 " - " GAL f 6 " " NAG f 7 " - " GAL f 8 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " MAN g 4 " - " NAG g 6 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " MAN r 4 " - " NAG r 6 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG s 5 " - " GAL s 6 " " NAG s 7 " - " GAL s 8 " BETA1-6 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 3 " " NAG f 1 " - " FUC f 10 " " MAN f 4 " - " NAG f 7 " " NAG g 1 " - " FUC g 9 " " NAG r 1 " - " FUC r 9 " " NAG s 1 " - " FUC s 9 " " MAN s 4 " - " NAG s 7 " NAG-ASN " NAG A 607 " - " ASN A 448 " " NAG A 612 " - " ASN A 234 " " NAG A 617 " - " ASN A 356 " " NAG A 628 " - " ASN A 301 " " NAG B1000 " - " ASN B 616 " " NAG B1003 " - " ASN B 637 " " NAG B1004 " - " ASN B 625 " " NAG C 601 " - " ASN C 356 " " NAG C 611 " - " ASN C 392 " " NAG C 612 " - " ASN C 276 " " NAG C 613 " - " ASN C 234 " " NAG C 614 " - " ASN C 88 " " NAG D1019 " - " ASN D 616 " " NAG D1020 " - " ASN D 625 " " NAG E 618 " - " ASN E 356 " " NAG E 619 " - " ASN E 88 " " NAG E 620 " - " ASN E 392 " " NAG E 623 " - " ASN E 234 " " NAG E 630 " - " ASN E 197 " " NAG F 901 " - " ASN F 625 " " NAG F 902 " - " ASN F 616 " " NAG G 1 " - " ASN A 197 " " NAG I 1 " - " ASN A 332 " " NAG J 1 " - " ASN A 295 " " NAG K 1 " - " ASN A 130 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 88 " " NAG R 1 " - " ASN A 392 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 197 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 130 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN C 295 " " NAG b 1 " - " ASN C 448 " " NAG c 1 " - " ASN C 262 " " NAG d 1 " - " ASN C 301 " " NAG e 1 " - " ASN C 386 " " NAG f 1 " - " ASN D 611 " " NAG g 1 " - " ASN D 637 " " NAG h 1 " - " ASN E 295 " " NAG i 1 " - " ASN E 301 " " NAG j 1 " - " ASN E 156 " " NAG k 1 " - " ASN E 262 " " NAG l 1 " - " ASN E 448 " " NAG m 1 " - " ASN E 332 " " NAG n 1 " - " ASN E 386 " " NAG o 1 " - " ASN E 276 " " NAG p 1 " - " ASN E 160 " " NAG r 1 " - " ASN F 637 " " NAG s 1 " - " ASN F 611 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.2 seconds 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 42 sheets defined 17.7% alpha, 29.4% 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 98 through 115 removed outlier: 4.122A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 removed outlier: 3.849A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.558A pdb=" N LEU A 181 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.573A pdb=" N GLU A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.504A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.738A pdb=" N SER A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 532 through 535 removed outlier: 3.869A pdb=" N LEU B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.319A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 536 through 542' Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.626A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.812A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.700A pdb=" N GLN B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 removed outlier: 4.137A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 3.542A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 336 through 350 removed outlier: 3.575A pdb=" N ALA C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.672A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.703A pdb=" N SER C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 544 removed outlier: 3.639A pdb=" N GLN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 565 removed outlier: 3.757A pdb=" N LEU D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 591 removed outlier: 3.695A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 582 " --> pdb=" O ALA D 578 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 596 removed outlier: 3.753A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 628 through 636 removed outlier: 4.001A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER D 636 " --> pdb=" O ASP D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 660 removed outlier: 3.635A pdb=" N TYR D 644 " --> pdb=" O ASP D 640 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 645 " --> pdb=" O THR D 641 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 659 " --> pdb=" O VAL D 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.575A pdb=" N CYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.745A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.590A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.127A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.672A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.096A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.708A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 631 through 636 Processing helix chain 'F' and resid 638 through 660 removed outlier: 3.581A pdb=" N LEU F 645 " --> pdb=" O THR F 641 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 removed outlier: 3.565A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.413A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.683A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.805A pdb=" N VAL A 120 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.013A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A 334 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.377A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 7.143A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 498 removed outlier: 5.147A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.709A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.507A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.836A pdb=" N HIS C 66 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.923A pdb=" N VAL C 120 " --> pdb=" O GLN C 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AB7, first strand: chain 'C' and resid 170 through 172 removed outlier: 3.519A pdb=" N CYS C 131 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 181 through 182 Processing sheet with id=AB9, first strand: chain 'C' and resid 358 through 361 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 358 through 361 current: chain 'C' and resid 441 through 456 removed outlier: 6.163A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.163A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLY C 441 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.133A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N ILE C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N VAL C 286 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 315 through 323 removed outlier: 3.839A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER C 334 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.302A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.980A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 66 through 67 removed outlier: 7.472A pdb=" N HIS E 66 " --> pdb=" O SER E 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 93 through 94 Processing sheet with id=AC7, first strand: chain 'E' and resid 129 through 131 removed outlier: 3.514A pdb=" N CYS E 131 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 154 through 162 Processing sheet with id=AC9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.591A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 271 through 273 removed outlier: 4.078A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 394 through 395 removed outlier: 5.947A pdb=" N THR E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE E 468 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY E 441 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 298 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 374 through 377 removed outlier: 4.529A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER E 334 " --> pdb=" O ARG E 293 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 298 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY E 441 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 305 through 308 Processing sheet with id=AD5, first strand: chain 'F' and resid 513 through 518 removed outlier: 3.527A pdb=" N GLY F 514 " --> pdb=" O TYR M 100M" (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASN M 100K" --> pdb=" O GLY F 516 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG M 100J" --> pdb=" O ASP M 100E" (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AD7, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.551A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.647A pdb=" N VAL H 37 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AE1, first strand: chain 'L' and resid 53 through 54 removed outlier: 4.149A pdb=" N GLU L 50 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR L 34 " --> pdb=" O MET L 89 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET L 89 " --> pdb=" O TYR L 34 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 66 through 67 Processing sheet with id=AE3, first strand: chain 'M' and resid 3 through 7 removed outlier: 4.470A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL M 18 " --> pdb=" O MET M 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET M 82 " --> pdb=" O VAL M 18 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU M 80 " --> pdb=" O LEU M 20 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.515A pdb=" N ALA M 93 " --> pdb=" O TYR M 35 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.723A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR N 72 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER N 65 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL N 63 " --> pdb=" O ARG N 74 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.669A pdb=" N LEU N 11 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR N 86 " --> pdb=" O THR N 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1393 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: 3.80 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5900 1.34 - 1.47: 5255 1.47 - 1.60: 8366 1.60 - 1.73: 0 1.73 - 1.86: 149 Bond restraints: 19670 Sorted by residual: bond pdb=" C VAL E 411 " pdb=" N PRO E 411B" ideal model delta sigma weight residual 1.334 1.391 -0.058 8.40e-03 1.42e+04 4.73e+01 bond pdb=" C PHE C 468 " pdb=" N ARG C 469 " ideal model delta sigma weight residual 1.333 1.249 0.083 2.74e-02 1.33e+03 9.26e+00 bond pdb=" CA ASN E 295 " pdb=" CB ASN E 295 " ideal model delta sigma weight residual 1.533 1.598 -0.065 2.29e-02 1.91e+03 7.96e+00 bond pdb=" C1 NAG E 620 " pdb=" O5 NAG E 620 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.04e+00 bond pdb=" C5 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.418 1.471 -0.053 2.00e-02 2.50e+03 6.93e+00 ... (remaining 19665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 25044 2.02 - 4.05: 1369 4.05 - 6.07: 206 6.07 - 8.09: 61 8.09 - 10.12: 14 Bond angle restraints: 26694 Sorted by residual: angle pdb=" C ASN E 295 " pdb=" CA ASN E 295 " pdb=" CB ASN E 295 " ideal model delta sigma weight residual 109.37 117.92 -8.55 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C THR H 107 " pdb=" N THR H 108 " pdb=" CA THR H 108 " ideal model delta sigma weight residual 122.82 129.08 -6.26 1.42e+00 4.96e-01 1.94e+01 angle pdb=" C LYS A 269 " pdb=" N VAL A 270 " pdb=" CA VAL A 270 " ideal model delta sigma weight residual 121.97 129.91 -7.94 1.80e+00 3.09e-01 1.94e+01 angle pdb=" C TRP F 628 " pdb=" N LEU F 629 " pdb=" CA LEU F 629 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C VAL E 505 " pdb=" N VAL E 506 " pdb=" CA VAL E 506 " ideal model delta sigma weight residual 121.70 129.12 -7.42 1.80e+00 3.09e-01 1.70e+01 ... (remaining 26689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.39: 12966 23.39 - 46.78: 385 46.78 - 70.16: 84 70.16 - 93.55: 47 93.55 - 116.94: 27 Dihedral angle restraints: 13509 sinusoidal: 7072 harmonic: 6437 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -161.26 75.26 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.59 -61.59 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS E 131 " pdb=" SG CYS E 131 " pdb=" SG CYS E 157 " pdb=" CB CYS E 157 " ideal model delta sinusoidal sigma weight residual 93.00 37.87 55.13 1 1.00e+01 1.00e-02 4.11e+01 ... (remaining 13506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 3349 0.197 - 0.394: 37 0.394 - 0.591: 7 0.591 - 0.789: 0 0.789 - 0.986: 1 Chirality restraints: 3394 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 332 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 130 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 386 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.33e+00 ... (remaining 3391 not shown) Planarity restraints: 3258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 479 " -0.022 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" CG TRP E 479 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP E 479 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP E 479 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 479 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP E 479 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 479 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 479 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 479 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 479 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 356 " -0.031 2.00e-02 2.50e+03 2.97e-02 1.11e+01 pdb=" CG ASN E 356 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN E 356 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 356 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG E 618 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 93 " -0.025 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE A 93 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 93 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 93 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 93 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 93 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 93 " -0.004 2.00e-02 2.50e+03 ... (remaining 3255 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 48 2.43 - 3.05: 11311 3.05 - 3.67: 25997 3.67 - 4.28: 40820 4.28 - 4.90: 67113 Nonbonded interactions: 145289 Sorted by model distance: nonbonded pdb=" OE1 GLU C 335 " pdb=" C ASN C 411C" model vdw 1.817 3.270 nonbonded pdb=" OE1 GLU C 335 " pdb=" CB ASN C 411C" model vdw 1.855 3.440 nonbonded pdb=" OE1 GLU C 335 " pdb=" CA ASN C 411C" model vdw 1.964 3.470 nonbonded pdb=" OE1 GLU C 335 " pdb=" O ASN C 411C" model vdw 1.989 3.040 nonbonded pdb=" ND2 ASN E 130 " pdb=" O5 NAG q 1 " model vdw 2.072 3.120 ... (remaining 145284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 165 or resid 167 through 172 or resid 174 throu \ gh 185 or resid 188 through 443 or resid 445 through 457 or resid 464 through 50 \ 6 or resid 607 through 628)) selection = (chain 'C' and (resid 32 through 58 or resid 71 through 136 or resid 147 through \ 165 or resid 167 through 172 or resid 174 through 398 or resid 411 through 443 \ or resid 445 through 457 or resid 464 through 506 or resid 611 through 614)) selection = (chain 'E' and (resid 32 through 58 or resid 71 through 136 or resid 147 through \ 165 or resid 167 through 172 or resid 174 through 185 or resid 188 through 443 \ or resid 445 through 457 or resid 464 through 506 or resid 619 through 630)) } ncs_group { reference = (chain 'B' and (resid 512 through 655 or resid 1003 through 1004)) selection = (chain 'F' and (resid 512 through 549 or resid 572 through 655 or resid 901 thro \ ugh 902)) } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'l' and resid 1) selection = (chain 'm' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'p' and resid 1) selection = (chain 'q' and resid 1) } ncs_group { reference = chain 'H' selection = (chain 'M' and resid 2 through 111) } ncs_group { reference = (chain 'L' and resid 2 through 105) selection = (chain 'N' and resid 2 through 105) } ncs_group { reference = (chain 'S' and (resid 1 or resid 4 through 6)) selection = (chain 'k' and (resid 2 or resid 5 through 7)) } ncs_group { reference = (chain 'f' and (resid 2 or resid 10)) selection = (chain 'g' and (resid 1 or resid 9)) selection = (chain 'r' and (resid 1 or resid 9)) selection = (chain 's' and (resid 1 or resid 9)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.150 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.199 19841 Z= 0.372 Angle : 1.168 17.895 27158 Z= 0.556 Chirality : 0.071 0.986 3394 Planarity : 0.007 0.069 3203 Dihedral : 13.004 116.940 9259 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.34 % Favored : 91.56 % Rotamer: Outliers : 0.36 % Allowed : 1.99 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.14), residues: 2192 helix: -4.37 (0.11), residues: 364 sheet: -2.55 (0.19), residues: 573 loop : -2.69 (0.14), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 298 TYR 0.038 0.003 TYR C 191 PHE 0.057 0.005 PHE A 93 TRP 0.057 0.005 TRP E 479 HIS 0.013 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00813 (19670) covalent geometry : angle 1.07289 (26694) SS BOND : bond 0.03465 ( 34) SS BOND : angle 1.99723 ( 68) hydrogen bonds : bond 0.30669 ( 481) hydrogen bonds : angle 10.71677 ( 1393) Misc. bond : bond 0.00206 ( 5) link_ALPHA1-2 : bond 0.00572 ( 2) link_ALPHA1-2 : angle 2.68650 ( 6) link_ALPHA1-3 : bond 0.00680 ( 7) link_ALPHA1-3 : angle 2.34603 ( 21) link_ALPHA1-6 : bond 0.00254 ( 7) link_ALPHA1-6 : angle 1.70124 ( 21) link_BETA1-2 : bond 0.00587 ( 6) link_BETA1-2 : angle 1.49053 ( 18) link_BETA1-4 : bond 0.00895 ( 47) link_BETA1-4 : angle 3.05540 ( 141) link_BETA1-6 : bond 0.00554 ( 8) link_BETA1-6 : angle 1.68320 ( 24) link_NAG-ASN : bond 0.00759 ( 55) link_NAG-ASN : angle 5.14978 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 467 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.7290 (t0) cc_final: 0.7030 (t70) REVERT: B 513 VAL cc_start: 0.9002 (t) cc_final: 0.8731 (m) REVERT: B 639 THR cc_start: 0.9013 (m) cc_final: 0.8808 (p) REVERT: C 426 MET cc_start: 0.8357 (tpt) cc_final: 0.8123 (tpt) REVERT: D 657 GLU cc_start: 0.8116 (pp20) cc_final: 0.7883 (pp20) REVERT: E 330 TYR cc_start: 0.8645 (p90) cc_final: 0.8415 (p90) REVERT: F 633 LYS cc_start: 0.8781 (mttt) cc_final: 0.8531 (mptt) REVERT: H 23 VAL cc_start: 0.7240 (t) cc_final: 0.6962 (m) REVERT: L 4 MET cc_start: 0.7686 (mmm) cc_final: 0.7355 (mmp) REVERT: L 92 LYS cc_start: 0.8873 (tmtm) cc_final: 0.8608 (tttm) REVERT: M 13 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7308 (mp10) REVERT: M 53 ASP cc_start: 0.7878 (t0) cc_final: 0.7606 (t0) REVERT: N 75 ILE cc_start: 0.8464 (mt) cc_final: 0.8144 (mt) REVERT: N 83 VAL cc_start: 0.8970 (m) cc_final: 0.8658 (t) outliers start: 5 outliers final: 0 residues processed: 470 average time/residue: 0.1767 time to fit residues: 119.8845 Evaluate side-chains 275 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 276 ASN A 352 HIS A 411CASN A 425 ASN A 478 ASN B 619 GLN C 72 HIS C 103 GLN C 146 ASN C 216 HIS C 374 HIS C 428 GLN D 540 GLN D 552 GLN D 607 ASN D 656 ASN E 32 ASN E 103 GLN E 187 ASN E 280 ASN E 348 GLN E 432 GLN F 540 GLN F 575 GLN F 619 GLN F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 53 ASN N 6 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.140284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108788 restraints weight = 78932.572| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 4.12 r_work: 0.3205 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 19841 Z= 0.231 Angle : 0.886 15.435 27158 Z= 0.420 Chirality : 0.054 0.496 3394 Planarity : 0.006 0.060 3203 Dihedral : 11.818 89.265 5115 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.19 % Allowed : 7.81 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % 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: -3.36 (0.15), residues: 2192 helix: -2.36 (0.21), residues: 371 sheet: -2.00 (0.20), residues: 592 loop : -2.31 (0.15), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 444 TYR 0.025 0.002 TYR C 191 PHE 0.028 0.003 PHE A 53 TRP 0.031 0.002 TRP A 479 HIS 0.006 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00556 (19670) covalent geometry : angle 0.80655 (26694) SS BOND : bond 0.00569 ( 34) SS BOND : angle 1.85361 ( 68) hydrogen bonds : bond 0.06062 ( 481) hydrogen bonds : angle 6.45616 ( 1393) Misc. bond : bond 0.00049 ( 5) link_ALPHA1-2 : bond 0.00499 ( 2) link_ALPHA1-2 : angle 2.25714 ( 6) link_ALPHA1-3 : bond 0.01123 ( 7) link_ALPHA1-3 : angle 1.66828 ( 21) link_ALPHA1-6 : bond 0.00724 ( 7) link_ALPHA1-6 : angle 1.86814 ( 21) link_BETA1-2 : bond 0.00224 ( 6) link_BETA1-2 : angle 1.51175 ( 18) link_BETA1-4 : bond 0.00491 ( 47) link_BETA1-4 : angle 2.15058 ( 141) link_BETA1-6 : bond 0.00409 ( 8) link_BETA1-6 : angle 1.58800 ( 24) link_NAG-ASN : bond 0.00547 ( 55) link_NAG-ASN : angle 4.12315 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 307 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8583 (tpp) cc_final: 0.8344 (tpp) REVERT: B 513 VAL cc_start: 0.9118 (t) cc_final: 0.8905 (m) REVERT: B 621 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8122 (tm-30) REVERT: C 121 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8636 (tppt) REVERT: C 378 CYS cc_start: 0.7150 (t) cc_final: 0.6814 (t) REVERT: C 426 MET cc_start: 0.8768 (tpt) cc_final: 0.8471 (tpt) REVERT: C 432 GLN cc_start: 0.8445 (mt0) cc_final: 0.8150 (mp10) REVERT: E 72 HIS cc_start: 0.7667 (p90) cc_final: 0.7309 (p-80) REVERT: F 545 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9045 (tp) REVERT: H 91 ARG cc_start: 0.7400 (mmt90) cc_final: 0.7197 (mmt90) REVERT: M 13 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7385 (mp10) REVERT: M 53 ASP cc_start: 0.8197 (t0) cc_final: 0.7851 (t0) REVERT: M 79 TYR cc_start: 0.8497 (m-80) cc_final: 0.8246 (m-80) REVERT: N 24 LYS cc_start: 0.8235 (tptt) cc_final: 0.7412 (mtmm) REVERT: N 39 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7117 (mmtt) REVERT: N 82 ASP cc_start: 0.7391 (m-30) cc_final: 0.7164 (m-30) outliers start: 41 outliers final: 23 residues processed: 325 average time/residue: 0.1649 time to fit residues: 79.2906 Evaluate side-chains 290 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 2 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 195 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN D 656 ASN E 32 ASN E 374 HIS E 478 ASN F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.139359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.107423 restraints weight = 93526.112| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 5.51 r_work: 0.3164 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 19841 Z= 0.191 Angle : 0.814 14.701 27158 Z= 0.380 Chirality : 0.051 0.453 3394 Planarity : 0.005 0.080 3203 Dihedral : 10.750 79.135 5115 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.40 % Allowed : 9.64 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % 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: -2.75 (0.16), residues: 2192 helix: -1.17 (0.25), residues: 371 sheet: -1.78 (0.20), residues: 574 loop : -2.07 (0.16), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 293 TYR 0.025 0.002 TYR C 191 PHE 0.024 0.002 PHE N 49 TRP 0.015 0.002 TRP E 338 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00451 (19670) covalent geometry : angle 0.73313 (26694) SS BOND : bond 0.00722 ( 34) SS BOND : angle 2.23681 ( 68) hydrogen bonds : bond 0.05085 ( 481) hydrogen bonds : angle 5.84031 ( 1393) Misc. bond : bond 0.00053 ( 5) link_ALPHA1-2 : bond 0.00555 ( 2) link_ALPHA1-2 : angle 2.13705 ( 6) link_ALPHA1-3 : bond 0.01183 ( 7) link_ALPHA1-3 : angle 1.42626 ( 21) link_ALPHA1-6 : bond 0.00772 ( 7) link_ALPHA1-6 : angle 1.85047 ( 21) link_BETA1-2 : bond 0.00229 ( 6) link_BETA1-2 : angle 1.58505 ( 18) link_BETA1-4 : bond 0.00502 ( 47) link_BETA1-4 : angle 2.05161 ( 141) link_BETA1-6 : bond 0.00375 ( 8) link_BETA1-6 : angle 1.39966 ( 24) link_NAG-ASN : bond 0.00506 ( 55) link_NAG-ASN : angle 3.87768 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 280 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 513 VAL cc_start: 0.9132 (t) cc_final: 0.8924 (m) REVERT: B 621 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8104 (tm-30) REVERT: C 121 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8722 (tppt) REVERT: C 378 CYS cc_start: 0.7305 (t) cc_final: 0.6975 (t) REVERT: C 426 MET cc_start: 0.8779 (tpt) cc_final: 0.8490 (tpt) REVERT: E 72 HIS cc_start: 0.7610 (p90) cc_final: 0.7284 (p-80) REVERT: E 486 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7130 (p90) REVERT: F 545 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9038 (tp) REVERT: H 30 SER cc_start: 0.9164 (OUTLIER) cc_final: 0.8963 (t) REVERT: L 103 LYS cc_start: 0.6542 (mmtt) cc_final: 0.6306 (mmmm) REVERT: M 13 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7479 (mp10) REVERT: M 53 ASP cc_start: 0.8200 (t0) cc_final: 0.7853 (t0) REVERT: N 24 LYS cc_start: 0.8365 (tptt) cc_final: 0.7435 (mtmm) outliers start: 45 outliers final: 31 residues processed: 300 average time/residue: 0.1683 time to fit residues: 75.0563 Evaluate side-chains 291 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 620 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 20 optimal weight: 0.0470 chunk 62 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 118 optimal weight: 0.0980 chunk 194 optimal weight: 9.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 203 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS D 656 ASN E 195 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN M 3 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.105981 restraints weight = 87591.988| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 5.03 r_work: 0.3218 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19841 Z= 0.128 Angle : 0.731 14.943 27158 Z= 0.336 Chirality : 0.049 0.408 3394 Planarity : 0.004 0.053 3203 Dihedral : 9.493 68.486 5115 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.04 % Allowed : 10.82 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.25 (0.17), residues: 2192 helix: -0.39 (0.27), residues: 363 sheet: -1.49 (0.20), residues: 580 loop : -1.86 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 46 TYR 0.020 0.001 TYR C 191 PHE 0.021 0.002 PHE N 49 TRP 0.013 0.001 TRP E 338 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00289 (19670) covalent geometry : angle 0.65795 (26694) SS BOND : bond 0.00542 ( 34) SS BOND : angle 1.50026 ( 68) hydrogen bonds : bond 0.03969 ( 481) hydrogen bonds : angle 5.39877 ( 1393) Misc. bond : bond 0.00070 ( 5) link_ALPHA1-2 : bond 0.00525 ( 2) link_ALPHA1-2 : angle 2.12750 ( 6) link_ALPHA1-3 : bond 0.01227 ( 7) link_ALPHA1-3 : angle 1.45503 ( 21) link_ALPHA1-6 : bond 0.00989 ( 7) link_ALPHA1-6 : angle 1.79681 ( 21) link_BETA1-2 : bond 0.00185 ( 6) link_BETA1-2 : angle 1.52283 ( 18) link_BETA1-4 : bond 0.00526 ( 47) link_BETA1-4 : angle 1.82219 ( 141) link_BETA1-6 : bond 0.00364 ( 8) link_BETA1-6 : angle 1.27082 ( 24) link_NAG-ASN : bond 0.00498 ( 55) link_NAG-ASN : angle 3.57151 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ILE cc_start: 0.9317 (mt) cc_final: 0.9093 (pt) REVERT: A 446 ASP cc_start: 0.8092 (m-30) cc_final: 0.7808 (m-30) REVERT: A 475 MET cc_start: 0.8730 (tpp) cc_final: 0.8457 (tpp) REVERT: B 513 VAL cc_start: 0.9091 (t) cc_final: 0.8888 (m) REVERT: B 621 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8180 (tm-30) REVERT: C 378 CYS cc_start: 0.7327 (t) cc_final: 0.6989 (t) REVERT: E 72 HIS cc_start: 0.7635 (p90) cc_final: 0.7259 (p-80) REVERT: E 133 ASN cc_start: 0.8318 (p0) cc_final: 0.8059 (m-40) REVERT: E 486 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7654 (p90) REVERT: F 545 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9268 (tm) REVERT: L 75 ILE cc_start: 0.5955 (mm) cc_final: 0.5524 (mt) REVERT: M 13 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7348 (mp10) REVERT: M 53 ASP cc_start: 0.8223 (t0) cc_final: 0.7898 (t0) REVERT: N 24 LYS cc_start: 0.8359 (tptt) cc_final: 0.7502 (mtmm) REVERT: N 92 LYS cc_start: 0.8755 (tptm) cc_final: 0.8542 (tptm) outliers start: 38 outliers final: 24 residues processed: 322 average time/residue: 0.1614 time to fit residues: 78.2545 Evaluate side-chains 294 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 268 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 130 ASN Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 83 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 214 optimal weight: 0.1980 chunk 73 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS C 72 HIS D 656 ASN E 249 HIS ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.137043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.105854 restraints weight = 83329.527| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.72 r_work: 0.3134 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 19841 Z= 0.264 Angle : 0.866 14.962 27158 Z= 0.402 Chirality : 0.053 0.470 3394 Planarity : 0.005 0.053 3203 Dihedral : 9.711 69.654 5115 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.11 % Allowed : 11.63 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.23 (0.17), residues: 2192 helix: -0.54 (0.26), residues: 378 sheet: -1.34 (0.21), residues: 565 loop : -1.88 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 273 TYR 0.028 0.002 TYR C 191 PHE 0.027 0.003 PHE A 93 TRP 0.016 0.002 TRP E 45 HIS 0.008 0.002 HIS H 56 Details of bonding type rmsd covalent geometry : bond 0.00634 (19670) covalent geometry : angle 0.79065 (26694) SS BOND : bond 0.00764 ( 34) SS BOND : angle 2.11676 ( 68) hydrogen bonds : bond 0.05060 ( 481) hydrogen bonds : angle 5.51385 ( 1393) Misc. bond : bond 0.00066 ( 5) link_ALPHA1-2 : bond 0.00433 ( 2) link_ALPHA1-2 : angle 2.26273 ( 6) link_ALPHA1-3 : bond 0.01140 ( 7) link_ALPHA1-3 : angle 1.56058 ( 21) link_ALPHA1-6 : bond 0.00769 ( 7) link_ALPHA1-6 : angle 1.95862 ( 21) link_BETA1-2 : bond 0.00376 ( 6) link_BETA1-2 : angle 1.69454 ( 18) link_BETA1-4 : bond 0.00497 ( 47) link_BETA1-4 : angle 2.12871 ( 141) link_BETA1-6 : bond 0.00484 ( 8) link_BETA1-6 : angle 1.67967 ( 24) link_NAG-ASN : bond 0.00497 ( 55) link_NAG-ASN : angle 3.87463 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 263 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 621 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8351 (tm-30) REVERT: C 121 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8671 (tppt) REVERT: C 368 ASP cc_start: 0.7995 (p0) cc_final: 0.7722 (p0) REVERT: C 378 CYS cc_start: 0.7456 (t) cc_final: 0.7201 (t) REVERT: E 72 HIS cc_start: 0.7592 (p90) cc_final: 0.7211 (p-80) REVERT: E 133 ASN cc_start: 0.8568 (p0) cc_final: 0.8210 (m-40) REVERT: F 545 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9302 (tm) REVERT: F 620 ASP cc_start: 0.8681 (t0) cc_final: 0.8419 (t0) REVERT: H 67 PHE cc_start: 0.8544 (m-10) cc_final: 0.8252 (m-80) REVERT: L 39 LYS cc_start: 0.7691 (mtpp) cc_final: 0.7414 (mtpp) REVERT: L 89 MET cc_start: 0.7336 (tpp) cc_final: 0.6802 (tpp) REVERT: M 13 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7375 (mp10) REVERT: M 53 ASP cc_start: 0.8339 (t0) cc_final: 0.7999 (t0) REVERT: N 24 LYS cc_start: 0.8407 (tptt) cc_final: 0.7505 (mtmm) REVERT: N 74 ARG cc_start: 0.8184 (ttt-90) cc_final: 0.7948 (tmt-80) outliers start: 59 outliers final: 47 residues processed: 297 average time/residue: 0.1703 time to fit residues: 74.8023 Evaluate side-chains 299 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 250 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 620 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS D 656 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.138670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105907 restraints weight = 73699.652| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.17 r_work: 0.3186 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19841 Z= 0.152 Angle : 0.757 14.814 27158 Z= 0.348 Chirality : 0.050 0.414 3394 Planarity : 0.004 0.049 3203 Dihedral : 9.109 67.336 5115 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.30 % Allowed : 12.81 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.09 % 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: -1.99 (0.17), residues: 2192 helix: -0.21 (0.27), residues: 376 sheet: -1.17 (0.21), residues: 577 loop : -1.78 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 304 TYR 0.022 0.001 TYR C 191 PHE 0.022 0.002 PHE N 49 TRP 0.012 0.001 TRP M 103 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00355 (19670) covalent geometry : angle 0.68373 (26694) SS BOND : bond 0.00523 ( 34) SS BOND : angle 1.81085 ( 68) hydrogen bonds : bond 0.04083 ( 481) hydrogen bonds : angle 5.27589 ( 1393) Misc. bond : bond 0.00055 ( 5) link_ALPHA1-2 : bond 0.00405 ( 2) link_ALPHA1-2 : angle 2.27191 ( 6) link_ALPHA1-3 : bond 0.01241 ( 7) link_ALPHA1-3 : angle 1.52338 ( 21) link_ALPHA1-6 : bond 0.01006 ( 7) link_ALPHA1-6 : angle 1.80414 ( 21) link_BETA1-2 : bond 0.00173 ( 6) link_BETA1-2 : angle 1.54397 ( 18) link_BETA1-4 : bond 0.00505 ( 47) link_BETA1-4 : angle 1.85539 ( 141) link_BETA1-6 : bond 0.00343 ( 8) link_BETA1-6 : angle 1.34912 ( 24) link_NAG-ASN : bond 0.00454 ( 55) link_NAG-ASN : angle 3.59865 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.8061 (m-30) cc_final: 0.7834 (m-30) REVERT: A 475 MET cc_start: 0.8742 (tpp) cc_final: 0.8511 (tpp) REVERT: B 621 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8384 (tm-30) REVERT: C 368 ASP cc_start: 0.7824 (p0) cc_final: 0.7510 (p0) REVERT: C 378 CYS cc_start: 0.7443 (t) cc_final: 0.7191 (t) REVERT: E 72 HIS cc_start: 0.7566 (p90) cc_final: 0.7180 (p-80) REVERT: E 133 ASN cc_start: 0.8395 (p0) cc_final: 0.8149 (m-40) REVERT: E 153 GLU cc_start: 0.7919 (pp20) cc_final: 0.7295 (pp20) REVERT: E 486 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7401 (p90) REVERT: F 530 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8510 (ttt) REVERT: F 545 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9037 (tp) REVERT: F 620 ASP cc_start: 0.8575 (t0) cc_final: 0.8295 (t0) REVERT: L 39 LYS cc_start: 0.7711 (mtpp) cc_final: 0.7382 (mtpp) REVERT: M 13 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7270 (mp10) REVERT: M 53 ASP cc_start: 0.8169 (t0) cc_final: 0.7834 (t0) REVERT: N 24 LYS cc_start: 0.8389 (tptt) cc_final: 0.7574 (mtmm) REVERT: N 61 ARG cc_start: 0.7847 (ptm160) cc_final: 0.7522 (ptp-170) REVERT: N 74 ARG cc_start: 0.8110 (ttt-90) cc_final: 0.7886 (tmt-80) REVERT: N 92 LYS cc_start: 0.8794 (tptm) cc_final: 0.8590 (tptm) outliers start: 43 outliers final: 37 residues processed: 299 average time/residue: 0.1604 time to fit residues: 71.6664 Evaluate side-chains 303 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 180 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 207 optimal weight: 0.2980 chunk 30 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN C 72 HIS D 656 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.139270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104056 restraints weight = 98027.898| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 4.89 r_work: 0.3175 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19841 Z= 0.134 Angle : 0.740 14.605 27158 Z= 0.339 Chirality : 0.049 0.406 3394 Planarity : 0.004 0.045 3203 Dihedral : 8.643 65.175 5115 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.70 % Allowed : 12.76 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % 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: -1.74 (0.17), residues: 2192 helix: 0.09 (0.28), residues: 370 sheet: -1.04 (0.21), residues: 574 loop : -1.62 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 100C TYR 0.020 0.001 TYR C 191 PHE 0.025 0.002 PHE H 67 TRP 0.011 0.001 TRP D 631 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00309 (19670) covalent geometry : angle 0.66839 (26694) SS BOND : bond 0.00529 ( 34) SS BOND : angle 1.96165 ( 68) hydrogen bonds : bond 0.03795 ( 481) hydrogen bonds : angle 5.16846 ( 1393) Misc. bond : bond 0.00052 ( 5) link_ALPHA1-2 : bond 0.00401 ( 2) link_ALPHA1-2 : angle 2.20873 ( 6) link_ALPHA1-3 : bond 0.01218 ( 7) link_ALPHA1-3 : angle 1.55189 ( 21) link_ALPHA1-6 : bond 0.01014 ( 7) link_ALPHA1-6 : angle 1.74817 ( 21) link_BETA1-2 : bond 0.00186 ( 6) link_BETA1-2 : angle 1.54182 ( 18) link_BETA1-4 : bond 0.00515 ( 47) link_BETA1-4 : angle 1.81873 ( 141) link_BETA1-6 : bond 0.00324 ( 8) link_BETA1-6 : angle 1.33141 ( 24) link_NAG-ASN : bond 0.00454 ( 55) link_NAG-ASN : angle 3.45688 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 271 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8293 (m-40) cc_final: 0.7832 (m-40) REVERT: A 446 ASP cc_start: 0.8118 (m-30) cc_final: 0.7856 (m-30) REVERT: A 475 MET cc_start: 0.8795 (tpp) cc_final: 0.8547 (tpp) REVERT: B 621 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8423 (tm-30) REVERT: B 651 ASN cc_start: 0.8298 (m-40) cc_final: 0.8097 (m-40) REVERT: C 378 CYS cc_start: 0.7604 (t) cc_final: 0.7354 (t) REVERT: E 72 HIS cc_start: 0.7623 (p90) cc_final: 0.7212 (p-80) REVERT: E 153 GLU cc_start: 0.7897 (pp20) cc_final: 0.7385 (pp20) REVERT: E 199 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.8370 (p) REVERT: E 486 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7414 (p90) REVERT: F 530 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8585 (ttt) REVERT: F 545 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9266 (tm) REVERT: F 620 ASP cc_start: 0.8701 (t0) cc_final: 0.8414 (t0) REVERT: H 64 GLN cc_start: 0.8336 (tp-100) cc_final: 0.8052 (tp-100) REVERT: L 39 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7385 (mtpp) REVERT: L 89 MET cc_start: 0.7152 (tpp) cc_final: 0.6623 (tpp) REVERT: M 13 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7305 (mp10) REVERT: M 53 ASP cc_start: 0.8206 (t0) cc_final: 0.7865 (t0) REVERT: N 24 LYS cc_start: 0.8395 (tptt) cc_final: 0.7562 (mtmm) REVERT: N 74 ARG cc_start: 0.8088 (ttt-90) cc_final: 0.7848 (tmt-80) outliers start: 51 outliers final: 36 residues processed: 297 average time/residue: 0.1605 time to fit residues: 71.4257 Evaluate side-chains 301 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 123 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 135 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 134 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 195 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS D 656 ASN F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.105824 restraints weight = 86691.543| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 4.66 r_work: 0.3214 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19841 Z= 0.119 Angle : 0.710 14.457 27158 Z= 0.325 Chirality : 0.048 0.394 3394 Planarity : 0.004 0.045 3203 Dihedral : 7.995 62.449 5115 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.09 % Allowed : 13.83 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % 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: -1.57 (0.17), residues: 2192 helix: 0.29 (0.28), residues: 368 sheet: -0.92 (0.21), residues: 580 loop : -1.53 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 100C TYR 0.018 0.001 TYR C 191 PHE 0.017 0.002 PHE N 49 TRP 0.012 0.001 TRP M 103 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00266 (19670) covalent geometry : angle 0.64311 (26694) SS BOND : bond 0.00591 ( 34) SS BOND : angle 1.79456 ( 68) hydrogen bonds : bond 0.03446 ( 481) hydrogen bonds : angle 4.99958 ( 1393) Misc. bond : bond 0.00050 ( 5) link_ALPHA1-2 : bond 0.00414 ( 2) link_ALPHA1-2 : angle 2.12550 ( 6) link_ALPHA1-3 : bond 0.01311 ( 7) link_ALPHA1-3 : angle 1.52765 ( 21) link_ALPHA1-6 : bond 0.01105 ( 7) link_ALPHA1-6 : angle 1.67889 ( 21) link_BETA1-2 : bond 0.00202 ( 6) link_BETA1-2 : angle 1.46396 ( 18) link_BETA1-4 : bond 0.00523 ( 47) link_BETA1-4 : angle 1.74534 ( 141) link_BETA1-6 : bond 0.00345 ( 8) link_BETA1-6 : angle 1.24082 ( 24) link_NAG-ASN : bond 0.00470 ( 55) link_NAG-ASN : angle 3.30184 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 287 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8188 (m-40) cc_final: 0.7738 (m-40) REVERT: A 444 ARG cc_start: 0.7523 (tmt-80) cc_final: 0.7321 (tpt170) REVERT: A 446 ASP cc_start: 0.7947 (m-30) cc_final: 0.7501 (m-30) REVERT: A 475 MET cc_start: 0.8781 (tpp) cc_final: 0.8544 (tpp) REVERT: B 621 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8380 (tm-30) REVERT: C 378 CYS cc_start: 0.7552 (t) cc_final: 0.7298 (t) REVERT: D 542 ARG cc_start: 0.8293 (ttp-170) cc_final: 0.8011 (mtp85) REVERT: D 620 ASP cc_start: 0.8016 (t70) cc_final: 0.7749 (t0) REVERT: D 621 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8066 (tm-30) REVERT: E 72 HIS cc_start: 0.7665 (p90) cc_final: 0.7228 (p-80) REVERT: E 153 GLU cc_start: 0.7779 (pp20) cc_final: 0.7193 (pp20) REVERT: E 486 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7438 (p90) REVERT: F 545 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9255 (tm) REVERT: F 620 ASP cc_start: 0.8628 (t0) cc_final: 0.8354 (t0) REVERT: H 81 GLU cc_start: 0.7624 (tp30) cc_final: 0.7068 (mm-30) REVERT: L 39 LYS cc_start: 0.7858 (mtpp) cc_final: 0.7488 (mtpp) REVERT: L 75 ILE cc_start: 0.5780 (mm) cc_final: 0.5349 (mt) REVERT: M 13 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7226 (mp10) REVERT: M 53 ASP cc_start: 0.8186 (t0) cc_final: 0.7873 (t0) REVERT: N 24 LYS cc_start: 0.8367 (tptt) cc_final: 0.7587 (mtmm) REVERT: N 61 ARG cc_start: 0.7739 (mtm180) cc_final: 0.7279 (ptm-80) REVERT: N 74 ARG cc_start: 0.8097 (ttt-90) cc_final: 0.7866 (tmt-80) outliers start: 39 outliers final: 30 residues processed: 304 average time/residue: 0.1615 time to fit residues: 73.1136 Evaluate side-chains 300 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 217 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN C 72 HIS D 656 ASN E 279 ASN F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108116 restraints weight = 93908.263| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 5.32 r_work: 0.3155 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19841 Z= 0.168 Angle : 0.753 14.497 27158 Z= 0.346 Chirality : 0.049 0.429 3394 Planarity : 0.004 0.043 3203 Dihedral : 8.029 62.519 5115 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.45 % Allowed : 14.13 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % 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: -1.55 (0.17), residues: 2192 helix: 0.23 (0.28), residues: 369 sheet: -0.87 (0.22), residues: 562 loop : -1.52 (0.16), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 100C TYR 0.025 0.002 TYR C 177 PHE 0.018 0.002 PHE N 49 TRP 0.013 0.001 TRP A 96 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00397 (19670) covalent geometry : angle 0.68507 (26694) SS BOND : bond 0.00523 ( 34) SS BOND : angle 1.90510 ( 68) hydrogen bonds : bond 0.03935 ( 481) hydrogen bonds : angle 5.04791 ( 1393) Misc. bond : bond 0.00048 ( 5) link_ALPHA1-2 : bond 0.00363 ( 2) link_ALPHA1-2 : angle 2.16683 ( 6) link_ALPHA1-3 : bond 0.01214 ( 7) link_ALPHA1-3 : angle 1.53762 ( 21) link_ALPHA1-6 : bond 0.00964 ( 7) link_ALPHA1-6 : angle 1.78901 ( 21) link_BETA1-2 : bond 0.00210 ( 6) link_BETA1-2 : angle 1.47827 ( 18) link_BETA1-4 : bond 0.00487 ( 47) link_BETA1-4 : angle 1.85355 ( 141) link_BETA1-6 : bond 0.00343 ( 8) link_BETA1-6 : angle 1.42788 ( 24) link_NAG-ASN : bond 0.00419 ( 55) link_NAG-ASN : angle 3.39760 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8235 (m-40) cc_final: 0.7785 (m-40) REVERT: B 621 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8455 (tm-30) REVERT: C 378 CYS cc_start: 0.7662 (t) cc_final: 0.7423 (t) REVERT: D 542 ARG cc_start: 0.8347 (ttp-170) cc_final: 0.8079 (mtp85) REVERT: D 620 ASP cc_start: 0.8139 (t70) cc_final: 0.7852 (t0) REVERT: D 621 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8077 (tm-30) REVERT: E 72 HIS cc_start: 0.7646 (p90) cc_final: 0.7217 (p-80) REVERT: E 153 GLU cc_start: 0.7852 (pp20) cc_final: 0.7228 (pp20) REVERT: E 486 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7120 (p90) REVERT: F 545 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9273 (tm) REVERT: F 620 ASP cc_start: 0.8686 (t0) cc_final: 0.8431 (t0) REVERT: H 81 GLU cc_start: 0.7776 (tp30) cc_final: 0.7266 (mm-30) REVERT: L 39 LYS cc_start: 0.7830 (mtpp) cc_final: 0.7391 (mtpp) REVERT: M 13 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7343 (mp10) REVERT: M 53 ASP cc_start: 0.8221 (t0) cc_final: 0.7865 (t0) REVERT: N 24 LYS cc_start: 0.8326 (tptt) cc_final: 0.7556 (mtmm) REVERT: N 61 ARG cc_start: 0.7791 (mtm180) cc_final: 0.7161 (ptm-80) REVERT: N 62 PHE cc_start: 0.7344 (m-80) cc_final: 0.7135 (m-80) REVERT: N 74 ARG cc_start: 0.8120 (ttt-90) cc_final: 0.7869 (tmt-80) REVERT: N 75 ILE cc_start: 0.7805 (mt) cc_final: 0.7577 (tt) outliers start: 46 outliers final: 38 residues processed: 287 average time/residue: 0.1511 time to fit residues: 65.2773 Evaluate side-chains 298 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 258 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 93 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN C 72 HIS D 656 ASN F 651 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.137234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102273 restraints weight = 86332.935| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 4.61 r_work: 0.3149 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19841 Z= 0.196 Angle : 0.787 14.583 27158 Z= 0.362 Chirality : 0.050 0.443 3394 Planarity : 0.005 0.097 3203 Dihedral : 8.216 63.203 5115 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.40 % Allowed : 14.18 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.05 % 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: -1.61 (0.17), residues: 2192 helix: 0.07 (0.27), residues: 372 sheet: -0.85 (0.22), residues: 575 loop : -1.55 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 100C TYR 0.022 0.002 TYR C 191 PHE 0.020 0.002 PHE N 49 TRP 0.014 0.002 TRP A 96 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd covalent geometry : bond 0.00467 (19670) covalent geometry : angle 0.71848 (26694) SS BOND : bond 0.00579 ( 34) SS BOND : angle 1.99358 ( 68) hydrogen bonds : bond 0.04231 ( 481) hydrogen bonds : angle 5.12800 ( 1393) Misc. bond : bond 0.00062 ( 5) link_ALPHA1-2 : bond 0.00317 ( 2) link_ALPHA1-2 : angle 2.29628 ( 6) link_ALPHA1-3 : bond 0.01203 ( 7) link_ALPHA1-3 : angle 1.53536 ( 21) link_ALPHA1-6 : bond 0.00957 ( 7) link_ALPHA1-6 : angle 1.81472 ( 21) link_BETA1-2 : bond 0.00203 ( 6) link_BETA1-2 : angle 1.51877 ( 18) link_BETA1-4 : bond 0.00504 ( 47) link_BETA1-4 : angle 1.90854 ( 141) link_BETA1-6 : bond 0.00375 ( 8) link_BETA1-6 : angle 1.48604 ( 24) link_NAG-ASN : bond 0.00428 ( 55) link_NAG-ASN : angle 3.47778 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.8356 (m-40) cc_final: 0.7878 (m-40) REVERT: B 621 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8432 (tm-30) REVERT: C 378 CYS cc_start: 0.7562 (t) cc_final: 0.7328 (t) REVERT: D 620 ASP cc_start: 0.8137 (t70) cc_final: 0.7811 (t0) REVERT: D 621 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7996 (tm-30) REVERT: E 153 GLU cc_start: 0.7854 (pp20) cc_final: 0.7229 (pp20) REVERT: E 486 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.6928 (p90) REVERT: F 545 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9293 (tm) REVERT: F 620 ASP cc_start: 0.8714 (t0) cc_final: 0.8477 (t0) REVERT: H 81 GLU cc_start: 0.7829 (tp30) cc_final: 0.7294 (mm-30) REVERT: H 82 MET cc_start: 0.7504 (mmm) cc_final: 0.7253 (mmm) REVERT: L 39 LYS cc_start: 0.7809 (mtpp) cc_final: 0.7397 (mtpp) REVERT: M 13 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7394 (mp10) REVERT: M 53 ASP cc_start: 0.8236 (t0) cc_final: 0.7874 (t0) REVERT: N 24 LYS cc_start: 0.8367 (tptt) cc_final: 0.7611 (mtmm) REVERT: N 61 ARG cc_start: 0.7733 (mtm180) cc_final: 0.7059 (ptm-80) REVERT: N 74 ARG cc_start: 0.8110 (ttt-90) cc_final: 0.7847 (tmt-80) REVERT: N 75 ILE cc_start: 0.7875 (mt) cc_final: 0.7590 (tt) outliers start: 45 outliers final: 42 residues processed: 288 average time/residue: 0.1622 time to fit residues: 69.4772 Evaluate side-chains 302 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 155 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 137 optimal weight: 0.2980 chunk 159 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN C 72 HIS D 656 ASN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.140697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109227 restraints weight = 92071.620| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 5.28 r_work: 0.3188 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19841 Z= 0.123 Angle : 0.721 14.359 27158 Z= 0.330 Chirality : 0.048 0.403 3394 Planarity : 0.004 0.089 3203 Dihedral : 7.792 61.192 5115 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.09 % Allowed : 14.69 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.44 (0.17), residues: 2192 helix: 0.26 (0.28), residues: 374 sheet: -0.74 (0.21), residues: 579 loop : -1.46 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 100C TYR 0.025 0.001 TYR B 644 PHE 0.017 0.002 PHE N 49 TRP 0.011 0.001 TRP D 631 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00281 (19670) covalent geometry : angle 0.65696 (26694) SS BOND : bond 0.00481 ( 34) SS BOND : angle 1.66201 ( 68) hydrogen bonds : bond 0.03519 ( 481) hydrogen bonds : angle 4.99022 ( 1393) Misc. bond : bond 0.00097 ( 5) link_ALPHA1-2 : bond 0.00359 ( 2) link_ALPHA1-2 : angle 2.22047 ( 6) link_ALPHA1-3 : bond 0.01242 ( 7) link_ALPHA1-3 : angle 1.47351 ( 21) link_ALPHA1-6 : bond 0.01045 ( 7) link_ALPHA1-6 : angle 1.73010 ( 21) link_BETA1-2 : bond 0.00191 ( 6) link_BETA1-2 : angle 1.43356 ( 18) link_BETA1-4 : bond 0.00515 ( 47) link_BETA1-4 : angle 1.73065 ( 141) link_BETA1-6 : bond 0.00337 ( 8) link_BETA1-6 : angle 1.25471 ( 24) link_NAG-ASN : bond 0.00466 ( 55) link_NAG-ASN : angle 3.27888 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5404.14 seconds wall clock time: 93 minutes 17.22 seconds (5597.22 seconds total)