Starting phenix.real_space_refine on Thu Feb 5 22:25:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhw_46884/02_2026/9dhw_46884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhw_46884/02_2026/9dhw_46884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dhw_46884/02_2026/9dhw_46884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhw_46884/02_2026/9dhw_46884.map" model { file = "/net/cci-nas-00/data/ceres_data/9dhw_46884/02_2026/9dhw_46884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhw_46884/02_2026/9dhw_46884.cif" } resolution = 3.35 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= 0.001 sd= 0.079 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 121 5.16 5 C 12776 2.51 5 N 3364 2.21 5 O 4122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20383 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3495 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1012 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3504 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Chain: "D" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 973 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1015 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "F" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 836 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 101} Chain: "G" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3486 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "H" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1015 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 836 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 101} Chain: "M" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 822 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "N" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1026 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "J" 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: "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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" 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: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 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: "W" 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" 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: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.23, per 1000 atoms: 0.26 Number of scatterers: 20383 At special positions: 0 Unit cell: (126.48, 147.56, 181.288, 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 121 16.00 O 4122 8.00 N 3364 7.00 C 12776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.07 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=2.07 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.06 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.10 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.06 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.06 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 27C" - pdb=" SG CYS F 28 " distance=2.14 Simple disulfide: pdb=" SG CYS F 89 " - pdb=" SG CYS F 96 " distance=1.72 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.05 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.08 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.06 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.05 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.14 Simple disulfide: pdb=" SG CYS L 27C" - pdb=" SG CYS L 28 " distance=2.19 Simple disulfide: pdb=" SG CYS L 89 " - pdb=" SG CYS L 96 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.14 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN W 4 " - " MAN W 5 " " MAN b 4 " - " MAN b 5 " " MAN g 4 " - " MAN g 5 " ALPHA1-3 " BMA J 3 " - " MAN J 6 " " MAN J 4 " - " MAN J 5 " " BMA O 3 " - " MAN O 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 4 " " MAN b 6 " - " MAN b 7 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA J 3 " - " MAN J 4 " " BMA O 3 " - " MAN O 7 " " BMA V 3 " - " MAN V 5 " " BMA b 3 " - " MAN b 6 " " MAN b 6 " - " MAN b 8 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " BETA1-6 " NAG T 1 " - " FUC T 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG f 1 " - " FUC f 4 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 197 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 448 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 133 " " NAG A 607 " - " ASN A 465 " " NAG A 608 " - " ASN A 241 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 392 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG G 601 " - " ASN G 160 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 301 " " NAG G 604 " - " ASN G 276 " " NAG G 605 " - " ASN G 241 " " NAG G 606 " - " ASN G 392 " " NAG G 607 " - " ASN G 448 " " NAG J 1 " - " ASN A 88 " " NAG K 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 332 " " NAG R 1 " - " ASN A 386 " " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN B 625 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN C 276 " " NAG a 1 " - " ASN C 301 " " NAG b 1 " - " ASN C 88 " " NAG c 1 " - " ASN C 465 " " NAG d 1 " - " ASN C 197 " " NAG e 1 " - " ASN C 386 " " NAG f 1 " - " ASN D 625 " " NAG g 1 " - " ASN G 262 " " NAG h 1 " - " ASN G 88 " " NAG i 1 " - " ASN G 156 " " NAG j 1 " - " ASN G 386 " " NAG k 1 " - " ASN G 465 " " NAG l 1 " - " ASN G 332 " " NAG m 1 " - " ASN G 234 " " NAG n 1 " - " ASN G 197 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 852.6 milliseconds 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4444 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 36 sheets defined 21.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.571A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.675A pdb=" N THR A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 484 removed outlier: 4.404A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.557A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.534A pdb=" N LYS B 574 " --> pdb=" O HIS B 570 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.513A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.182A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.845A pdb=" N THR C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.624A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.515A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.954A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 597 Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.576A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.505A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.695A pdb=" N THR G 351 " --> pdb=" O GLU G 347 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 475 through 484 removed outlier: 4.369A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.558A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 65 removed outlier: 4.546A pdb=" N ASP H 65 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.741A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 596 Processing helix chain 'I' and resid 618 through 626 removed outlier: 3.642A pdb=" N MET I 626 " --> pdb=" O ILE I 622 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 658 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.889A pdb=" N SER M 31 " --> pdb=" O VAL M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.973A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 73 through 75 No H-bonds generated for 'chain 'N' and resid 73 through 75' Processing helix chain 'N' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.387A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.688A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.915A pdb=" N HIS A 66 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.589A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 4.085A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.187A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.091A 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: 4.599A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.350A 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 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.540A pdb=" N ARG C 169 " --> pdb=" O TYR N 100H" (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER N 100J" --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS C 171 " --> pdb=" O SER N 100J" (cutoff:3.500A) removed outlier: 13.512A pdb=" N THR N 100L" --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 18.498A pdb=" N TYR C 173 " --> pdb=" O THR N 100L" (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASP N 97 " --> pdb=" O GLY N 100I" (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.294A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.590A pdb=" N ASN C 301 " --> pdb=" O ILE C 322A" (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE C 322A" --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 27 current: chain 'E' and resid 73 through 82 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 12 current: chain 'E' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 58 current: chain 'E' and resid 100F through 103 Processing sheet with id=AC1, first strand: chain 'F' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 9 through 14 current: chain 'F' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 53 through 54 current: chain 'F' and resid 95 through 98 Processing sheet with id=AC2, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AC3, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.248A pdb=" N VAL I 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL G 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR I 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR G 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N CYS I 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'G' and resid 75 through 76 removed outlier: 6.883A pdb=" N CYS G 54 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AC8, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.264A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 283 through 298 removed outlier: 7.234A pdb=" N THR G 293 " --> pdb=" O THR G 334 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR G 334 " --> pdb=" O THR G 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 330 through 334 current: chain 'G' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 381 through 385 current: chain 'G' and resid 465 through 470 Processing sheet with id=AD1, first strand: chain 'G' and resid 301 through 312 removed outlier: 3.591A pdb=" N ASN G 301 " --> pdb=" O ILE G 323 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP G 322 " --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE G 309 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA G 316 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 18 through 27 current: chain 'H' and resid 73 through 82 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 58 current: chain 'H' and resid 100F through 103 Processing sheet with id=AD4, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AD5, first strand: chain 'L' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 14 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 95 through 98 Processing sheet with id=AD6, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'M' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 11 current: chain 'M' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 53 through 54 current: chain 'M' and resid 97 through 98 Processing sheet with id=AD8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'N' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 10 through 12 current: chain 'N' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 57 through 59 current: chain 'N' and resid 102 through 103 527 hydrogen bonds defined for protein. 1380 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: 3.47 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4909 1.33 - 1.46: 6309 1.46 - 1.59: 9437 1.59 - 1.72: 0 1.72 - 1.85: 156 Bond restraints: 20811 Sorted by residual: bond pdb=" N ILE M 58 " pdb=" CA ILE M 58 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.60e-03 1.73e+04 1.92e+01 bond pdb=" CB ILE A 201 " pdb=" CG1 ILE A 201 " ideal model delta sigma weight residual 1.530 1.463 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" N ILE M 48 " pdb=" CA ILE M 48 " ideal model delta sigma weight residual 1.458 1.498 -0.039 1.19e-02 7.06e+03 1.10e+01 bond pdb=" CB ILE G 201 " pdb=" CG1 ILE G 201 " ideal model delta sigma weight residual 1.530 1.467 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" N GLY C 263 " pdb=" CA GLY C 263 " ideal model delta sigma weight residual 1.442 1.466 -0.024 7.70e-03 1.69e+04 9.92e+00 ... (remaining 20806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 28003 4.70 - 9.39: 262 9.39 - 14.09: 1 14.09 - 18.79: 0 18.79 - 23.49: 1 Bond angle restraints: 28267 Sorted by residual: angle pdb=" C TYR M 91 " pdb=" CA TYR M 91 " pdb=" CB TYR M 91 " ideal model delta sigma weight residual 109.72 86.23 23.49 1.92e+00 2.71e-01 1.50e+02 angle pdb=" C SER L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 119.56 127.50 -7.94 1.02e+00 9.61e-01 6.06e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 127.44 -7.88 1.02e+00 9.61e-01 5.97e+01 angle pdb=" C ALA L 43 " pdb=" N PRO L 44 " pdb=" CA PRO L 44 " ideal model delta sigma weight residual 120.03 127.53 -7.50 9.90e-01 1.02e+00 5.74e+01 angle pdb=" C ALA F 43 " pdb=" N PRO F 44 " pdb=" CA PRO F 44 " ideal model delta sigma weight residual 119.78 127.49 -7.71 1.03e+00 9.43e-01 5.61e+01 ... (remaining 28262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 13278 21.25 - 42.49: 309 42.49 - 63.74: 80 63.74 - 84.98: 90 84.98 - 106.23: 47 Dihedral angle restraints: 13804 sinusoidal: 6882 harmonic: 6922 Sorted by residual: dihedral pdb=" C TYR M 91 " pdb=" N TYR M 91 " pdb=" CA TYR M 91 " pdb=" CB TYR M 91 " ideal model delta harmonic sigma weight residual -122.60 -92.99 -29.61 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" CB CYS F 89 " pdb=" SG CYS F 89 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 170.57 -77.57 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS L 89 " pdb=" SG CYS L 89 " pdb=" SG CYS L 96 " pdb=" CB CYS L 96 " ideal model delta sinusoidal sigma weight residual 93.00 167.62 -74.62 1 1.00e+01 1.00e-02 7.05e+01 ... (remaining 13801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 3150 0.116 - 0.232: 275 0.232 - 0.348: 28 0.348 - 0.463: 4 0.463 - 0.579: 3 Chirality restraints: 3460 Sorted by residual: chirality pdb=" C1 BMA W 3 " pdb=" O4 NAG W 2 " pdb=" C2 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-02 2.50e+03 8.39e+02 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.88e+02 chirality pdb=" C1 MAN J 4 " pdb=" O6 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 1.99 0.41 2.00e-02 2.50e+03 4.12e+02 ... (remaining 3457 not shown) Planarity restraints: 3491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 448 " 0.053 2.00e-02 2.50e+03 5.48e-02 3.75e+01 pdb=" CG ASN C 448 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN C 448 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 448 " -0.085 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 625 " -0.049 2.00e-02 2.50e+03 5.09e-02 3.24e+01 pdb=" CG ASN D 625 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN D 625 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN D 625 " 0.080 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 392 " 0.047 2.00e-02 2.50e+03 4.86e-02 2.96e+01 pdb=" CG ASN C 392 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 392 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN C 392 " -0.075 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " 0.058 2.00e-02 2.50e+03 ... (remaining 3488 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 654 2.70 - 3.25: 19571 3.25 - 3.80: 31714 3.80 - 4.35: 41997 4.35 - 4.90: 68559 Nonbonded interactions: 162495 Sorted by model distance: nonbonded pdb=" O3 NAG f 2 " pdb=" O7 NAG f 2 " model vdw 2.154 3.040 nonbonded pdb=" O3 NAG R 2 " pdb=" O7 NAG R 2 " model vdw 2.155 3.040 nonbonded pdb=" O6 NAG b 1 " pdb=" N2 NAG b 2 " model vdw 2.192 3.120 nonbonded pdb=" O3 NAG d 1 " pdb=" O5 NAG d 2 " model vdw 2.352 3.040 nonbonded pdb=" C3 NAG f 2 " pdb=" O7 NAG f 2 " model vdw 2.357 3.470 ... (remaining 162490 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 506 or resid 602 through 603)) selection = (chain 'C' and (resid 32 through 59 or resid 66 through 506 or resid 602 through \ 603)) selection = (chain 'G' and resid 32 through 602) } ncs_group { reference = (chain 'B' and (resid 520 through 543 or resid 570 through 659)) selection = (chain 'D' and (resid 520 through 543 or resid 570 through 659)) selection = (chain 'I' and (resid 520 through 543 or resid 570 through 659)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'L' } ncs_group { reference = (chain 'J' and (resid 1 or resid 4 through 6)) selection = (chain 'O' and (resid 2 or resid 5 through 7)) } ncs_group { reference = (chain 'K' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' 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 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'k' and resid 1) selection = (chain 'l' and resid 1) selection = (chain 'm' and resid 1) selection = (chain 'n' and resid 1) } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'h' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.280 Find NCS groups from input model: 0.570 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.013 0.314 20962 Z= 0.691 Angle : 1.401 23.487 28677 Z= 0.855 Chirality : 0.073 0.579 3460 Planarity : 0.005 0.041 3441 Dihedral : 13.704 106.231 9231 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.05 % Allowed : 0.33 % Favored : 99.62 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.09 % 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: 2.61 (0.17), residues: 2359 helix: -0.03 (0.22), residues: 425 sheet: 1.87 (0.19), residues: 653 loop : 2.63 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 54 TYR 0.061 0.004 TYR M 91 PHE 0.027 0.004 PHE N 100P TRP 0.034 0.006 TRP H 47 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.01201 (20811) covalent geometry : angle 1.28494 (28267) SS BOND : bond 0.06542 ( 43) SS BOND : angle 3.67110 ( 86) hydrogen bonds : bond 0.19301 ( 527) hydrogen bonds : angle 7.02322 ( 1380) link_ALPHA1-2 : bond 0.04589 ( 5) link_ALPHA1-2 : angle 5.70095 ( 15) link_ALPHA1-3 : bond 0.04674 ( 8) link_ALPHA1-3 : angle 5.02725 ( 24) link_ALPHA1-6 : bond 0.03678 ( 5) link_ALPHA1-6 : angle 4.41491 ( 15) link_BETA1-4 : bond 0.04691 ( 38) link_BETA1-4 : angle 6.59726 ( 114) link_BETA1-6 : bond 0.03829 ( 2) link_BETA1-6 : angle 3.17713 ( 6) link_NAG-ASN : bond 0.06754 ( 50) link_NAG-ASN : angle 3.67554 ( 150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 456 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 THR cc_start: 0.8400 (m) cc_final: 0.8142 (p) REVERT: C 504 ARG cc_start: 0.7532 (mtp180) cc_final: 0.7026 (mpt180) REVERT: G 213 ILE cc_start: 0.8655 (mt) cc_final: 0.8408 (tt) REVERT: H 66 ARG cc_start: 0.6836 (mtm180) cc_final: 0.6378 (mtp180) REVERT: I 601 LYS cc_start: 0.8747 (mttt) cc_final: 0.8229 (mtpt) REVERT: I 626 MET cc_start: 0.8331 (mtp) cc_final: 0.8126 (mtt) REVERT: N 110 THR cc_start: 0.8781 (m) cc_final: 0.8382 (p) outliers start: 1 outliers final: 0 residues processed: 456 average time/residue: 0.1679 time to fit residues: 113.8293 Evaluate side-chains 223 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 269 ASN B 575 GLN B 591 GLN C 33 ASN C 94 ASN C 269 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS E 58 ASN F 52 ASN G 99 ASN G 170 GLN H 82BASN M 90 GLN N 73 ASN N 76 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.131975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102575 restraints weight = 33552.914| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.96 r_work: 0.3236 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20962 Z= 0.175 Angle : 0.679 8.771 28677 Z= 0.335 Chirality : 0.045 0.235 3460 Planarity : 0.004 0.034 3441 Dihedral : 10.329 81.801 4796 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.23 % Allowed : 6.56 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.09 % 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: 2.42 (0.17), residues: 2359 helix: 1.55 (0.26), residues: 412 sheet: 1.60 (0.19), residues: 661 loop : 1.88 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 503 TYR 0.025 0.002 TYR M 91 PHE 0.023 0.002 PHE N 67 TRP 0.013 0.001 TRP E 50 HIS 0.006 0.001 HIS N 100F Details of bonding type rmsd covalent geometry : bond 0.00409 (20811) covalent geometry : angle 0.63298 (28267) SS BOND : bond 0.00459 ( 43) SS BOND : angle 1.56160 ( 86) hydrogen bonds : bond 0.05822 ( 527) hydrogen bonds : angle 5.29265 ( 1380) link_ALPHA1-2 : bond 0.00753 ( 5) link_ALPHA1-2 : angle 1.96767 ( 15) link_ALPHA1-3 : bond 0.01225 ( 8) link_ALPHA1-3 : angle 2.22696 ( 24) link_ALPHA1-6 : bond 0.00699 ( 5) link_ALPHA1-6 : angle 1.91834 ( 15) link_BETA1-4 : bond 0.00594 ( 38) link_BETA1-4 : angle 2.53429 ( 114) link_BETA1-6 : bond 0.00590 ( 2) link_BETA1-6 : angle 1.27741 ( 6) link_NAG-ASN : bond 0.00293 ( 50) link_NAG-ASN : angle 2.17910 ( 150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 THR cc_start: 0.8622 (m) cc_final: 0.8287 (p) REVERT: A 161 MET cc_start: 0.8471 (tpt) cc_final: 0.7923 (tpt) REVERT: A 425 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7094 (m-40) REVERT: A 475 MET cc_start: 0.9016 (tpp) cc_final: 0.8716 (tpp) REVERT: C 123 THR cc_start: 0.8364 (m) cc_final: 0.7923 (p) REVERT: C 340 LYS cc_start: 0.8153 (tttm) cc_final: 0.7799 (mmtm) REVERT: C 504 ARG cc_start: 0.7441 (mtp180) cc_final: 0.6797 (mpt180) REVERT: D 632 ASP cc_start: 0.8677 (t70) cc_final: 0.8451 (t0) REVERT: G 75 VAL cc_start: 0.7291 (t) cc_final: 0.6983 (m) REVERT: H 38 ARG cc_start: 0.6202 (ttp80) cc_final: 0.5986 (ptm-80) REVERT: H 82 ASN cc_start: 0.8406 (p0) cc_final: 0.8142 (p0) REVERT: I 530 MET cc_start: 0.8331 (mtp) cc_final: 0.7877 (mtp) REVERT: I 601 LYS cc_start: 0.8753 (mttt) cc_final: 0.8154 (mtpt) REVERT: I 655 LYS cc_start: 0.8426 (tppt) cc_final: 0.8207 (tppt) REVERT: L 73 LEU cc_start: 0.7203 (tt) cc_final: 0.6967 (tt) REVERT: M 78 LEU cc_start: 0.8577 (mp) cc_final: 0.8254 (mp) REVERT: N 100 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7534 (mt0) REVERT: N 110 THR cc_start: 0.8569 (m) cc_final: 0.8047 (p) outliers start: 47 outliers final: 28 residues processed: 292 average time/residue: 0.1501 time to fit residues: 67.8851 Evaluate side-chains 246 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 172 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 ASN G 99 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.129179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098456 restraints weight = 34221.426| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.24 r_work: 0.3154 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20962 Z= 0.187 Angle : 0.630 7.972 28677 Z= 0.313 Chirality : 0.046 0.216 3460 Planarity : 0.004 0.043 3441 Dihedral : 8.281 74.851 4796 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.23 % Allowed : 8.03 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.94 (0.17), residues: 2359 helix: 1.84 (0.27), residues: 402 sheet: 1.22 (0.19), residues: 661 loop : 1.34 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 503 TYR 0.029 0.002 TYR F 65 PHE 0.017 0.002 PHE N 67 TRP 0.015 0.001 TRP E 50 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00444 (20811) covalent geometry : angle 0.59524 (28267) SS BOND : bond 0.00488 ( 43) SS BOND : angle 1.21461 ( 86) hydrogen bonds : bond 0.05053 ( 527) hydrogen bonds : angle 4.87864 ( 1380) link_ALPHA1-2 : bond 0.00588 ( 5) link_ALPHA1-2 : angle 1.70446 ( 15) link_ALPHA1-3 : bond 0.01111 ( 8) link_ALPHA1-3 : angle 1.80331 ( 24) link_ALPHA1-6 : bond 0.00702 ( 5) link_ALPHA1-6 : angle 1.72057 ( 15) link_BETA1-4 : bond 0.00502 ( 38) link_BETA1-4 : angle 2.09010 ( 114) link_BETA1-6 : bond 0.00276 ( 2) link_BETA1-6 : angle 1.34190 ( 6) link_NAG-ASN : bond 0.00306 ( 50) link_NAG-ASN : angle 1.97016 ( 150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 237 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 THR cc_start: 0.8652 (m) cc_final: 0.8426 (p) REVERT: A 161 MET cc_start: 0.8545 (tpt) cc_final: 0.7913 (tpt) REVERT: A 475 MET cc_start: 0.9085 (tpp) cc_final: 0.8685 (tpp) REVERT: C 123 THR cc_start: 0.8302 (m) cc_final: 0.7924 (p) REVERT: C 340 LYS cc_start: 0.8159 (tttm) cc_final: 0.7778 (mmtm) REVERT: C 504 ARG cc_start: 0.7624 (mtp180) cc_final: 0.6952 (mpt180) REVERT: D 632 ASP cc_start: 0.8650 (t70) cc_final: 0.8394 (t0) REVERT: E 46 GLU cc_start: 0.7106 (pt0) cc_final: 0.6883 (pt0) REVERT: E 48 MET cc_start: 0.8174 (mtt) cc_final: 0.7888 (mtm) REVERT: F 66 LYS cc_start: 0.7799 (tptm) cc_final: 0.7548 (tptm) REVERT: G 75 VAL cc_start: 0.7483 (t) cc_final: 0.7221 (m) REVERT: H 38 ARG cc_start: 0.6404 (ttp80) cc_final: 0.5962 (ptm-80) REVERT: H 58 ASN cc_start: 0.8319 (t0) cc_final: 0.7994 (t0) REVERT: I 601 LYS cc_start: 0.8730 (mttt) cc_final: 0.8138 (mtpt) REVERT: M 78 LEU cc_start: 0.8491 (mp) cc_final: 0.8273 (mp) REVERT: M 79 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7837 (mp0) REVERT: N 100 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7598 (mt0) REVERT: N 110 THR cc_start: 0.8573 (m) cc_final: 0.8066 (p) outliers start: 47 outliers final: 33 residues processed: 268 average time/residue: 0.1536 time to fit residues: 63.9697 Evaluate side-chains 238 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 81 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 168 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 585 HIS D 651 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.127102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.095891 restraints weight = 34393.563| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.29 r_work: 0.3118 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20962 Z= 0.194 Angle : 0.609 8.092 28677 Z= 0.299 Chirality : 0.045 0.227 3460 Planarity : 0.004 0.047 3441 Dihedral : 7.189 69.666 4796 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.61 % Allowed : 8.79 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2359 helix: 1.84 (0.28), residues: 396 sheet: 1.00 (0.19), residues: 655 loop : 0.98 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 337 TYR 0.032 0.002 TYR M 91 PHE 0.018 0.002 PHE N 67 TRP 0.016 0.001 TRP E 50 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00465 (20811) covalent geometry : angle 0.57695 (28267) SS BOND : bond 0.00468 ( 43) SS BOND : angle 1.21915 ( 86) hydrogen bonds : bond 0.04739 ( 527) hydrogen bonds : angle 4.78535 ( 1380) link_ALPHA1-2 : bond 0.00562 ( 5) link_ALPHA1-2 : angle 1.60331 ( 15) link_ALPHA1-3 : bond 0.01116 ( 8) link_ALPHA1-3 : angle 1.82319 ( 24) link_ALPHA1-6 : bond 0.00720 ( 5) link_ALPHA1-6 : angle 1.67930 ( 15) link_BETA1-4 : bond 0.00447 ( 38) link_BETA1-4 : angle 1.85011 ( 114) link_BETA1-6 : bond 0.00407 ( 2) link_BETA1-6 : angle 1.36851 ( 6) link_NAG-ASN : bond 0.00312 ( 50) link_NAG-ASN : angle 1.87856 ( 150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8597 (tpt) cc_final: 0.7976 (tpt) REVERT: C 33 ASN cc_start: 0.7113 (p0) cc_final: 0.6832 (p0) REVERT: C 504 ARG cc_start: 0.7707 (mtp180) cc_final: 0.6996 (mpt180) REVERT: D 632 ASP cc_start: 0.8645 (t70) cc_final: 0.8383 (t0) REVERT: F 66 LYS cc_start: 0.7810 (tptm) cc_final: 0.7560 (tptm) REVERT: G 434 MET cc_start: 0.8619 (ttt) cc_final: 0.8408 (ttt) REVERT: H 38 ARG cc_start: 0.6101 (ttp80) cc_final: 0.5642 (ptm-80) REVERT: I 601 LYS cc_start: 0.8741 (mttt) cc_final: 0.8145 (mtpt) REVERT: M 78 LEU cc_start: 0.8549 (mp) cc_final: 0.8261 (mp) REVERT: M 79 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7215 (mp0) REVERT: N 100 ASP cc_start: 0.7320 (t0) cc_final: 0.7117 (t0) REVERT: N 100 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7604 (mt0) REVERT: N 108 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8522 (tp) outliers start: 55 outliers final: 40 residues processed: 248 average time/residue: 0.1415 time to fit residues: 55.5630 Evaluate side-chains 230 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 233 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 223 optimal weight: 0.4980 chunk 206 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 188 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100CGLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.096238 restraints weight = 34252.898| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.29 r_work: 0.3121 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20962 Z= 0.166 Angle : 0.575 7.747 28677 Z= 0.283 Chirality : 0.044 0.222 3460 Planarity : 0.003 0.046 3441 Dihedral : 6.704 72.054 4796 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.23 % Allowed : 9.93 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.40 (0.17), residues: 2359 helix: 1.91 (0.28), residues: 397 sheet: 0.84 (0.19), residues: 686 loop : 0.81 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 337 TYR 0.032 0.001 TYR M 91 PHE 0.013 0.002 PHE N 67 TRP 0.014 0.001 TRP L 38 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00395 (20811) covalent geometry : angle 0.54551 (28267) SS BOND : bond 0.00406 ( 43) SS BOND : angle 1.05204 ( 86) hydrogen bonds : bond 0.04442 ( 527) hydrogen bonds : angle 4.67415 ( 1380) link_ALPHA1-2 : bond 0.00540 ( 5) link_ALPHA1-2 : angle 1.64095 ( 15) link_ALPHA1-3 : bond 0.01154 ( 8) link_ALPHA1-3 : angle 1.80953 ( 24) link_ALPHA1-6 : bond 0.00743 ( 5) link_ALPHA1-6 : angle 1.77552 ( 15) link_BETA1-4 : bond 0.00434 ( 38) link_BETA1-4 : angle 1.67262 ( 114) link_BETA1-6 : bond 0.00328 ( 2) link_BETA1-6 : angle 1.28454 ( 6) link_NAG-ASN : bond 0.00262 ( 50) link_NAG-ASN : angle 1.78038 ( 150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8564 (tpt) cc_final: 0.7964 (tpt) REVERT: A 164 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: C 504 ARG cc_start: 0.7668 (mtp180) cc_final: 0.7071 (mpt180) REVERT: D 632 ASP cc_start: 0.8684 (t70) cc_final: 0.8424 (t0) REVERT: E 46 GLU cc_start: 0.7713 (pt0) cc_final: 0.7398 (pt0) REVERT: E 48 MET cc_start: 0.7967 (mtt) cc_final: 0.7524 (mtm) REVERT: F 66 LYS cc_start: 0.7800 (tptm) cc_final: 0.7458 (tptp) REVERT: I 530 MET cc_start: 0.8564 (mtp) cc_final: 0.8073 (mtp) REVERT: I 601 LYS cc_start: 0.8783 (mttt) cc_final: 0.8477 (mtpp) REVERT: M 61 ARG cc_start: 0.7281 (ttp-110) cc_final: 0.6653 (ttm170) REVERT: M 78 LEU cc_start: 0.8453 (mp) cc_final: 0.8162 (mp) REVERT: M 79 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7141 (mp0) REVERT: N 30 ASP cc_start: 0.8503 (m-30) cc_final: 0.8268 (m-30) REVERT: N 100 GLN cc_start: 0.8032 (mm110) cc_final: 0.7650 (mm-40) REVERT: N 108 LEU cc_start: 0.8797 (tp) cc_final: 0.8559 (tp) outliers start: 47 outliers final: 41 residues processed: 240 average time/residue: 0.1457 time to fit residues: 54.8886 Evaluate side-chains 234 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 162 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 224 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 221 optimal weight: 9.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** G 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.128825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098084 restraints weight = 33973.259| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.21 r_work: 0.3158 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20962 Z= 0.104 Angle : 0.528 9.524 28677 Z= 0.258 Chirality : 0.043 0.225 3460 Planarity : 0.003 0.042 3441 Dihedral : 6.099 70.878 4796 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.23 % Allowed : 10.40 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.49 (0.17), residues: 2359 helix: 2.09 (0.28), residues: 403 sheet: 0.87 (0.19), residues: 668 loop : 0.84 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 38 TYR 0.028 0.001 TYR M 91 PHE 0.010 0.001 PHE N 100P TRP 0.013 0.001 TRP L 38 HIS 0.003 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00232 (20811) covalent geometry : angle 0.50012 (28267) SS BOND : bond 0.00347 ( 43) SS BOND : angle 1.01829 ( 86) hydrogen bonds : bond 0.03856 ( 527) hydrogen bonds : angle 4.51472 ( 1380) link_ALPHA1-2 : bond 0.00571 ( 5) link_ALPHA1-2 : angle 1.70873 ( 15) link_ALPHA1-3 : bond 0.01190 ( 8) link_ALPHA1-3 : angle 1.81696 ( 24) link_ALPHA1-6 : bond 0.00778 ( 5) link_ALPHA1-6 : angle 1.89721 ( 15) link_BETA1-4 : bond 0.00456 ( 38) link_BETA1-4 : angle 1.49679 ( 114) link_BETA1-6 : bond 0.00364 ( 2) link_BETA1-6 : angle 1.21019 ( 6) link_NAG-ASN : bond 0.00171 ( 50) link_NAG-ASN : angle 1.60050 ( 150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8544 (tpt) cc_final: 0.7946 (tpt) REVERT: A 164 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: A 428 GLN cc_start: 0.7976 (mp10) cc_final: 0.7689 (mp10) REVERT: C 33 ASN cc_start: 0.7176 (p0) cc_final: 0.6962 (p0) REVERT: C 504 ARG cc_start: 0.7666 (mtp180) cc_final: 0.7041 (mpt180) REVERT: D 632 ASP cc_start: 0.8610 (t70) cc_final: 0.8377 (t0) REVERT: E 46 GLU cc_start: 0.7721 (pt0) cc_final: 0.7500 (pt0) REVERT: E 48 MET cc_start: 0.7839 (mtt) cc_final: 0.7419 (mtm) REVERT: E 72 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.8008 (t) REVERT: F 66 LYS cc_start: 0.7803 (tptm) cc_final: 0.7510 (tptp) REVERT: G 217 TYR cc_start: 0.7624 (m-80) cc_final: 0.7300 (m-80) REVERT: G 475 MET cc_start: 0.8328 (tpp) cc_final: 0.7970 (tpp) REVERT: I 601 LYS cc_start: 0.8759 (mttt) cc_final: 0.8424 (mtpp) REVERT: M 61 ARG cc_start: 0.7119 (ttp-110) cc_final: 0.6576 (ttm170) REVERT: M 78 LEU cc_start: 0.8509 (mp) cc_final: 0.8221 (mp) REVERT: M 79 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7138 (mp0) REVERT: N 30 ASP cc_start: 0.8409 (m-30) cc_final: 0.8195 (m-30) REVERT: N 100 GLN cc_start: 0.7869 (mm110) cc_final: 0.7532 (mp10) outliers start: 47 outliers final: 31 residues processed: 236 average time/residue: 0.1460 time to fit residues: 54.2082 Evaluate side-chains 225 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 7 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 79 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 134 optimal weight: 0.0170 chunk 99 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 230 optimal weight: 0.0870 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** G 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.128821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098093 restraints weight = 34162.767| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.25 r_work: 0.3154 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20962 Z= 0.115 Angle : 0.528 6.336 28677 Z= 0.259 Chirality : 0.043 0.226 3460 Planarity : 0.003 0.043 3441 Dihedral : 5.775 70.948 4796 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.81 % Allowed : 10.93 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.09 % 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: 1.44 (0.17), residues: 2359 helix: 2.19 (0.28), residues: 397 sheet: 0.87 (0.19), residues: 669 loop : 0.75 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 38 TYR 0.023 0.001 TYR F 65 PHE 0.011 0.001 PHE N 100P TRP 0.015 0.001 TRP L 38 HIS 0.003 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00266 (20811) covalent geometry : angle 0.50060 (28267) SS BOND : bond 0.00386 ( 43) SS BOND : angle 1.06662 ( 86) hydrogen bonds : bond 0.03835 ( 527) hydrogen bonds : angle 4.44613 ( 1380) link_ALPHA1-2 : bond 0.00565 ( 5) link_ALPHA1-2 : angle 1.66647 ( 15) link_ALPHA1-3 : bond 0.01114 ( 8) link_ALPHA1-3 : angle 1.76487 ( 24) link_ALPHA1-6 : bond 0.00737 ( 5) link_ALPHA1-6 : angle 1.68005 ( 15) link_BETA1-4 : bond 0.00438 ( 38) link_BETA1-4 : angle 1.48966 ( 114) link_BETA1-6 : bond 0.00392 ( 2) link_BETA1-6 : angle 1.22055 ( 6) link_NAG-ASN : bond 0.00188 ( 50) link_NAG-ASN : angle 1.58899 ( 150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8547 (tpt) cc_final: 0.7940 (tpt) REVERT: A 164 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: C 504 ARG cc_start: 0.7688 (mtp180) cc_final: 0.7090 (mpt180) REVERT: D 632 ASP cc_start: 0.8603 (t70) cc_final: 0.8367 (t0) REVERT: E 48 MET cc_start: 0.7895 (mtt) cc_final: 0.7176 (mtm) REVERT: E 72 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8008 (t) REVERT: F 49 TYR cc_start: 0.4321 (OUTLIER) cc_final: 0.3944 (m-10) REVERT: F 66 LYS cc_start: 0.7795 (tptm) cc_final: 0.7502 (tptp) REVERT: G 217 TYR cc_start: 0.7573 (m-80) cc_final: 0.7211 (m-80) REVERT: G 356 ASN cc_start: 0.7782 (m-40) cc_final: 0.7508 (p0) REVERT: G 426 MET cc_start: 0.7851 (mmt) cc_final: 0.7639 (mmt) REVERT: G 475 MET cc_start: 0.8402 (tpp) cc_final: 0.8029 (tpp) REVERT: I 601 LYS cc_start: 0.8765 (mttt) cc_final: 0.8459 (mtpp) REVERT: M 61 ARG cc_start: 0.7102 (ttp-110) cc_final: 0.6387 (ttp-110) REVERT: M 78 LEU cc_start: 0.8529 (mp) cc_final: 0.8238 (mp) REVERT: M 79 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7025 (mp0) REVERT: N 100 GLN cc_start: 0.7861 (mm110) cc_final: 0.7572 (mp10) outliers start: 38 outliers final: 27 residues processed: 230 average time/residue: 0.1383 time to fit residues: 50.6834 Evaluate side-chains 223 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 7 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 186 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 0.0070 chunk 163 optimal weight: 8.9990 chunk 195 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.124593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092877 restraints weight = 34450.829| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.23 r_work: 0.3080 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20962 Z= 0.250 Angle : 0.641 6.620 28677 Z= 0.315 Chirality : 0.047 0.256 3460 Planarity : 0.004 0.047 3441 Dihedral : 6.351 80.901 4796 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.04 % Allowed : 11.31 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.04 (0.17), residues: 2359 helix: 1.84 (0.28), residues: 398 sheet: 0.50 (0.19), residues: 665 loop : 0.57 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.025 0.002 TYR M 91 PHE 0.018 0.002 PHE B 522 TRP 0.024 0.002 TRP E 50 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00610 (20811) covalent geometry : angle 0.61003 (28267) SS BOND : bond 0.00505 ( 43) SS BOND : angle 1.40639 ( 86) hydrogen bonds : bond 0.04803 ( 527) hydrogen bonds : angle 4.73500 ( 1380) link_ALPHA1-2 : bond 0.00524 ( 5) link_ALPHA1-2 : angle 1.59290 ( 15) link_ALPHA1-3 : bond 0.00969 ( 8) link_ALPHA1-3 : angle 1.87903 ( 24) link_ALPHA1-6 : bond 0.00644 ( 5) link_ALPHA1-6 : angle 1.59552 ( 15) link_BETA1-4 : bond 0.00408 ( 38) link_BETA1-4 : angle 1.70523 ( 114) link_BETA1-6 : bond 0.00386 ( 2) link_BETA1-6 : angle 1.30328 ( 6) link_NAG-ASN : bond 0.00421 ( 50) link_NAG-ASN : angle 1.95596 ( 150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8592 (tpt) cc_final: 0.7960 (tpt) REVERT: A 164 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: C 504 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7182 (mpt180) REVERT: D 632 ASP cc_start: 0.8725 (t70) cc_final: 0.8439 (t0) REVERT: E 48 MET cc_start: 0.8027 (mtt) cc_final: 0.7374 (mtm) REVERT: F 49 TYR cc_start: 0.4869 (OUTLIER) cc_final: 0.4477 (m-10) REVERT: F 66 LYS cc_start: 0.7799 (tptm) cc_final: 0.7493 (tptp) REVERT: F 87 TYR cc_start: 0.7688 (m-80) cc_final: 0.7433 (m-80) REVERT: I 601 LYS cc_start: 0.8799 (mttt) cc_final: 0.8485 (mtpp) REVERT: M 61 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6751 (ttm170) REVERT: M 78 LEU cc_start: 0.8537 (mp) cc_final: 0.8230 (mp) REVERT: M 79 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7279 (mp0) REVERT: N 100 GLN cc_start: 0.7950 (mm110) cc_final: 0.7609 (mp10) outliers start: 43 outliers final: 35 residues processed: 220 average time/residue: 0.1303 time to fit residues: 45.5024 Evaluate side-chains 223 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 100 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 174 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 188 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.124614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.093394 restraints weight = 34413.751| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.21 r_work: 0.3087 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20962 Z= 0.206 Angle : 0.603 6.653 28677 Z= 0.298 Chirality : 0.045 0.246 3460 Planarity : 0.004 0.043 3441 Dihedral : 6.324 89.412 4796 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.14 % Allowed : 11.45 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.09 % 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: 0.85 (0.17), residues: 2359 helix: 1.79 (0.28), residues: 398 sheet: 0.28 (0.19), residues: 675 loop : 0.48 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 38 TYR 0.024 0.002 TYR M 91 PHE 0.015 0.002 PHE N 67 TRP 0.019 0.001 TRP E 50 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00498 (20811) covalent geometry : angle 0.57431 (28267) SS BOND : bond 0.00451 ( 43) SS BOND : angle 1.18276 ( 86) hydrogen bonds : bond 0.04513 ( 527) hydrogen bonds : angle 4.69853 ( 1380) link_ALPHA1-2 : bond 0.00490 ( 5) link_ALPHA1-2 : angle 1.66105 ( 15) link_ALPHA1-3 : bond 0.01048 ( 8) link_ALPHA1-3 : angle 1.83564 ( 24) link_ALPHA1-6 : bond 0.00671 ( 5) link_ALPHA1-6 : angle 1.63026 ( 15) link_BETA1-4 : bond 0.00400 ( 38) link_BETA1-4 : angle 1.59523 ( 114) link_BETA1-6 : bond 0.00312 ( 2) link_BETA1-6 : angle 1.38275 ( 6) link_NAG-ASN : bond 0.00314 ( 50) link_NAG-ASN : angle 1.85026 ( 150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8627 (tpt) cc_final: 0.8007 (tpt) REVERT: A 164 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: A 356 ASN cc_start: 0.7489 (m110) cc_final: 0.7222 (t0) REVERT: B 540 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8534 (mp10) REVERT: C 504 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7193 (mpt180) REVERT: D 632 ASP cc_start: 0.8676 (t70) cc_final: 0.8419 (t0) REVERT: D 648 GLU cc_start: 0.8486 (tp30) cc_final: 0.8227 (tt0) REVERT: F 49 TYR cc_start: 0.4924 (OUTLIER) cc_final: 0.4399 (m-10) REVERT: F 87 TYR cc_start: 0.7785 (m-80) cc_final: 0.7295 (m-80) REVERT: I 601 LYS cc_start: 0.8762 (mttt) cc_final: 0.8437 (mtpp) REVERT: M 61 ARG cc_start: 0.7184 (ttp-110) cc_final: 0.6582 (ttm170) REVERT: M 78 LEU cc_start: 0.8548 (mp) cc_final: 0.8264 (mp) REVERT: M 79 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7286 (mp0) REVERT: N 100 GLN cc_start: 0.7919 (mm110) cc_final: 0.7599 (mp10) outliers start: 45 outliers final: 36 residues processed: 221 average time/residue: 0.1353 time to fit residues: 47.6201 Evaluate side-chains 220 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 100 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 149 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN D 651 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.124671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.093434 restraints weight = 34627.799| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.23 r_work: 0.3087 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20962 Z= 0.193 Angle : 0.603 8.168 28677 Z= 0.299 Chirality : 0.045 0.251 3460 Planarity : 0.004 0.042 3441 Dihedral : 6.286 83.117 4796 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.04 % Allowed : 11.54 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.09 % 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: 0.81 (0.17), residues: 2359 helix: 1.85 (0.28), residues: 398 sheet: 0.25 (0.19), residues: 668 loop : 0.41 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.018 0.002 TYR M 91 PHE 0.014 0.002 PHE N 67 TRP 0.017 0.001 TRP E 50 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00467 (20811) covalent geometry : angle 0.57480 (28267) SS BOND : bond 0.00439 ( 43) SS BOND : angle 1.15074 ( 86) hydrogen bonds : bond 0.04470 ( 527) hydrogen bonds : angle 4.69022 ( 1380) link_ALPHA1-2 : bond 0.00485 ( 5) link_ALPHA1-2 : angle 1.66515 ( 15) link_ALPHA1-3 : bond 0.00996 ( 8) link_ALPHA1-3 : angle 1.82142 ( 24) link_ALPHA1-6 : bond 0.00687 ( 5) link_ALPHA1-6 : angle 1.58777 ( 15) link_BETA1-4 : bond 0.00401 ( 38) link_BETA1-4 : angle 1.59071 ( 114) link_BETA1-6 : bond 0.00346 ( 2) link_BETA1-6 : angle 1.36559 ( 6) link_NAG-ASN : bond 0.00320 ( 50) link_NAG-ASN : angle 1.85261 ( 150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8613 (tpt) cc_final: 0.7988 (tpt) REVERT: A 164 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: A 356 ASN cc_start: 0.7494 (m110) cc_final: 0.7233 (t0) REVERT: C 504 ARG cc_start: 0.7690 (mtp180) cc_final: 0.7159 (mpt180) REVERT: D 632 ASP cc_start: 0.8692 (t70) cc_final: 0.8425 (t0) REVERT: D 648 GLU cc_start: 0.8451 (tp30) cc_final: 0.8234 (tt0) REVERT: E 48 MET cc_start: 0.7880 (mtt) cc_final: 0.7092 (mtm) REVERT: F 49 TYR cc_start: 0.4977 (OUTLIER) cc_final: 0.4430 (m-10) REVERT: F 87 TYR cc_start: 0.7865 (m-80) cc_final: 0.7392 (m-80) REVERT: I 601 LYS cc_start: 0.8770 (mttt) cc_final: 0.8439 (mtpp) REVERT: M 61 ARG cc_start: 0.7236 (ttp-110) cc_final: 0.6691 (ttm170) REVERT: M 78 LEU cc_start: 0.8591 (mp) cc_final: 0.8316 (mp) REVERT: M 79 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7321 (mp0) REVERT: N 100 GLN cc_start: 0.7918 (mm110) cc_final: 0.7605 (mp10) outliers start: 43 outliers final: 39 residues processed: 211 average time/residue: 0.1220 time to fit residues: 41.4578 Evaluate side-chains 222 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain G residue 53 PHE Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 119 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 209 optimal weight: 0.4980 chunk 132 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.125597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094613 restraints weight = 34391.175| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.21 r_work: 0.3108 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20962 Z= 0.142 Angle : 0.565 6.974 28677 Z= 0.281 Chirality : 0.044 0.241 3460 Planarity : 0.003 0.040 3441 Dihedral : 6.118 79.408 4796 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.95 % Allowed : 11.73 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.09 % 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: 0.84 (0.17), residues: 2359 helix: 1.97 (0.28), residues: 398 sheet: 0.26 (0.20), residues: 656 loop : 0.40 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.024 0.001 TYR F 65 PHE 0.012 0.001 PHE N 67 TRP 0.016 0.001 TRP A 112 HIS 0.003 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00335 (20811) covalent geometry : angle 0.53805 (28267) SS BOND : bond 0.00391 ( 43) SS BOND : angle 1.03178 ( 86) hydrogen bonds : bond 0.04177 ( 527) hydrogen bonds : angle 4.61346 ( 1380) link_ALPHA1-2 : bond 0.00528 ( 5) link_ALPHA1-2 : angle 1.71216 ( 15) link_ALPHA1-3 : bond 0.01095 ( 8) link_ALPHA1-3 : angle 1.80986 ( 24) link_ALPHA1-6 : bond 0.00730 ( 5) link_ALPHA1-6 : angle 1.56213 ( 15) link_BETA1-4 : bond 0.00403 ( 38) link_BETA1-4 : angle 1.51626 ( 114) link_BETA1-6 : bond 0.00396 ( 2) link_BETA1-6 : angle 1.28299 ( 6) link_NAG-ASN : bond 0.00237 ( 50) link_NAG-ASN : angle 1.75134 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4307.29 seconds wall clock time: 74 minutes 58.15 seconds (4498.15 seconds total)