Starting phenix.real_space_refine on Tue May 20 14:04:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tkc_41346/05_2025/8tkc_41346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tkc_41346/05_2025/8tkc_41346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tkc_41346/05_2025/8tkc_41346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tkc_41346/05_2025/8tkc_41346.map" model { file = "/net/cci-nas-00/data/ceres_data/8tkc_41346/05_2025/8tkc_41346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tkc_41346/05_2025/8tkc_41346.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 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 123 5.16 5 C 12549 2.51 5 N 3336 2.21 5 O 4056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20064 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "G" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 980 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "H" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 99} Chain: "I" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 980 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "J" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 99} Chain: "K" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 980 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 99} 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 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: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: 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: "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: 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 12.42, per 1000 atoms: 0.62 Number of scatterers: 20064 At special positions: 0 Unit cell: (150.284, 142.51, 124.373, 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 123 16.00 O 4056 8.00 N 3336 7.00 C 12549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA m 3 " - " MAN m 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 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 R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " 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 g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 276 " " NAG Z 1 " - " ASN C 386 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 295 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 332 " " NAG f 1 " - " ASN C 363 " " NAG g 1 " - " ASN E 295 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 386 " " NAG m 1 " - " ASN E 262 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 332 " " NAG p 1 " - " ASN E 363 " Time building additional restraints: 5.80 Conformation dependent library (CDL) restraints added in 2.1 seconds 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 41 sheets defined 19.0% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.122A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.597A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.253A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.882A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.595A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.887A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 663 removed outlier: 3.724A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.162A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.551A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.920A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'D' and resid 521 through 527 removed outlier: 4.595A pdb=" N ALA D 525 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.985A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 639 through 663 removed outlier: 3.729A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.178A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.547A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.505A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 527 removed outlier: 4.549A pdb=" N ALA F 525 " --> pdb=" O PHE F 522 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.088A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.552A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.903A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 639 through 663 removed outlier: 3.750A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.869A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.863A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.860A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.314A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.039A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.352A 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 removed outlier: 3.567A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.398A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.051A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.600A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.571A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'B' and resid 516 through 519 removed outlier: 6.186A pdb=" N GLY B 516 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TYR G 99 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 518 " --> pdb=" O TYR G 99 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN G 95 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TYR G 34 " --> pdb=" O GLN G 95 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.596A pdb=" N VAL G 12 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.311A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.831A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.407A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.032A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.581A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 517 through 519 removed outlier: 6.646A pdb=" N VAL D 518 " --> pdb=" O TYR I 99 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN I 95 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR I 34 " --> pdb=" O GLN I 95 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP I 35 " --> pdb=" O ASN I 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.600A pdb=" N VAL I 12 " --> pdb=" O SER I 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.293A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.065A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.418A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.030A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.506A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.590A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD4, first strand: chain 'F' and resid 517 through 519 removed outlier: 6.737A pdb=" N VAL F 518 " --> pdb=" O TYR K 99 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN K 95 " --> pdb=" O TYR K 34 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR K 34 " --> pdb=" O GLN K 95 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP K 35 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN K 50 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.605A pdb=" N VAL K 12 " --> pdb=" O SER K 112 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.536A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.538A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.539A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.72 Time building geometry restraints manager: 6.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.26: 3199 1.26 - 1.61: 17107 1.61 - 1.97: 162 1.97 - 2.32: 0 2.32 - 2.67: 1 Bond restraints: 20469 Sorted by residual: bond pdb=" CB PRO A 498 " pdb=" CG PRO A 498 " ideal model delta sigma weight residual 1.492 2.675 -1.183 5.00e-02 4.00e+02 5.60e+02 bond pdb=" CG PRO A 498 " pdb=" CD PRO A 498 " ideal model delta sigma weight residual 1.503 0.908 0.595 3.40e-02 8.65e+02 3.06e+02 bond pdb=" C ALA A 497 " pdb=" N PRO A 498 " ideal model delta sigma weight residual 1.329 1.420 -0.090 1.25e-02 6.40e+03 5.22e+01 bond pdb=" CA PRO A 498 " pdb=" CB PRO A 498 " ideal model delta sigma weight residual 1.534 1.454 0.080 1.23e-02 6.61e+03 4.22e+01 bond pdb=" N PRO A 498 " pdb=" CD PRO A 498 " ideal model delta sigma weight residual 1.473 1.563 -0.090 1.40e-02 5.10e+03 4.17e+01 ... (remaining 20464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.92: 27806 19.92 - 39.84: 0 39.84 - 59.76: 0 59.76 - 79.68: 0 79.68 - 99.60: 1 Bond angle restraints: 27807 Sorted by residual: angle pdb=" CB PRO A 498 " pdb=" CG PRO A 498 " pdb=" CD PRO A 498 " ideal model delta sigma weight residual 106.10 6.50 99.60 3.20e+00 9.77e-02 9.69e+02 angle pdb=" N PRO A 498 " pdb=" CA PRO A 498 " pdb=" CB PRO A 498 " ideal model delta sigma weight residual 103.15 92.10 11.05 9.70e-01 1.06e+00 1.30e+02 angle pdb=" CA PRO A 498 " pdb=" CB PRO A 498 " pdb=" CG PRO A 498 " ideal model delta sigma weight residual 104.50 87.00 17.50 1.90e+00 2.77e-01 8.48e+01 angle pdb=" CA PRO A 498 " pdb=" N PRO A 498 " pdb=" CD PRO A 498 " ideal model delta sigma weight residual 112.00 100.68 11.32 1.40e+00 5.10e-01 6.54e+01 angle pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 114.40 132.09 -17.69 2.30e+00 1.89e-01 5.92e+01 ... (remaining 27802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.42: 12513 27.42 - 54.84: 686 54.84 - 82.26: 114 82.26 - 109.68: 42 109.68 - 137.10: 1 Dihedral angle restraints: 13356 sinusoidal: 6408 harmonic: 6948 Sorted by residual: dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 5.18 87.82 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual 93.00 26.04 66.96 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -21.97 -64.03 1 1.00e+01 1.00e-02 5.40e+01 ... (remaining 13353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2891 0.062 - 0.124: 403 0.124 - 0.187: 70 0.187 - 0.249: 2 0.249 - 0.311: 12 Chirality restraints: 3378 Sorted by residual: chirality pdb=" CA CYS E 296 " pdb=" N CYS E 296 " pdb=" C CYS E 296 " pdb=" CB CYS E 296 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 3375 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 239 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO C 240 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 240 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 240 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER I 100F" -0.038 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO I 100G" 0.101 5.00e-02 4.00e+02 pdb=" CA PRO I 100G" -0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 100G" -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 100F" -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO G 100G" 0.100 5.00e-02 4.00e+02 pdb=" CA PRO G 100G" -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 100G" -0.031 5.00e-02 4.00e+02 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 396 2.69 - 3.24: 17654 3.24 - 3.79: 28755 3.79 - 4.35: 39112 4.35 - 4.90: 67608 Nonbonded interactions: 153525 Sorted by model distance: nonbonded pdb=" OG1 THR A 139 " pdb=" OD1 ASP A 141 " model vdw 2.134 3.040 nonbonded pdb=" O PHE D 522 " pdb=" NE2 GLN D 540 " model vdw 2.188 3.120 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.194 3.040 nonbonded pdb=" O ASP H 82 " pdb=" OH TYR H 86 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR C 139 " pdb=" OD1 ASP C 141 " model vdw 2.223 3.040 ... (remaining 153520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'j' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'm' } 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: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 44.290 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.011 1.183 20598 Z= 0.316 Angle : 0.974 99.605 28152 Z= 0.417 Chirality : 0.049 0.311 3378 Planarity : 0.004 0.060 3429 Dihedral : 16.986 137.102 8754 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.61 % Favored : 97.26 % Rotamer: Outliers : 0.33 % Allowed : 13.44 % Favored : 86.23 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.17), residues: 2373 helix: 2.24 (0.29), residues: 396 sheet: 0.15 (0.18), residues: 777 loop : -0.87 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.004 0.001 HIS A 216 PHE 0.010 0.001 PHE A 53 TYR 0.036 0.001 TYR I 34 ARG 0.007 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 45) link_NAG-ASN : angle 2.23787 ( 135) link_BETA1-4 : bond 0.00480 ( 36) link_BETA1-4 : angle 1.01362 ( 108) link_ALPHA1-2 : bond 0.00321 ( 3) link_ALPHA1-2 : angle 1.60373 ( 9) link_ALPHA1-3 : bond 0.00556 ( 3) link_ALPHA1-3 : angle 1.46490 ( 9) hydrogen bonds : bond 0.10911 ( 735) hydrogen bonds : angle 5.34300 ( 1974) SS BOND : bond 0.00678 ( 42) SS BOND : angle 2.56207 ( 84) covalent geometry : bond 0.01055 (20469) covalent geometry : angle 0.95417 (27807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 GLU cc_start: 0.7881 (tp30) cc_final: 0.7666 (tp30) REVERT: C 268 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6719 (pm20) REVERT: E 268 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6627 (pm20) REVERT: E 475 MET cc_start: 0.8836 (mmp) cc_final: 0.8611 (tpp) REVERT: F 655 LYS cc_start: 0.6394 (ttpt) cc_final: 0.5967 (ttpt) outliers start: 7 outliers final: 5 residues processed: 182 average time/residue: 0.4169 time to fit residues: 107.5803 Evaluate side-chains 175 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain I residue 100 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 8.9990 chunk 179 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 185 optimal weight: 30.0000 chunk 71 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN D 653 GLN E 137 ASN E 355 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.204257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130494 restraints weight = 20798.829| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.69 r_work: 0.3095 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.977 20598 Z= 0.349 Angle : 1.011 106.097 28152 Z= 0.441 Chirality : 0.051 0.252 3378 Planarity : 0.005 0.083 3429 Dihedral : 11.756 91.998 4377 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.16 % Favored : 96.71 % Rotamer: Outliers : 1.98 % Allowed : 12.97 % Favored : 85.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2373 helix: 1.82 (0.28), residues: 399 sheet: 0.15 (0.18), residues: 804 loop : -0.97 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 427 HIS 0.005 0.001 HIS C 374 PHE 0.022 0.002 PHE A 383 TYR 0.014 0.002 TYR C 173 ARG 0.006 0.001 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 45) link_NAG-ASN : angle 2.60991 ( 135) link_BETA1-4 : bond 0.00953 ( 36) link_BETA1-4 : angle 1.46429 ( 108) link_ALPHA1-2 : bond 0.00592 ( 3) link_ALPHA1-2 : angle 1.55180 ( 9) link_ALPHA1-3 : bond 0.01640 ( 3) link_ALPHA1-3 : angle 0.79267 ( 9) hydrogen bonds : bond 0.05467 ( 735) hydrogen bonds : angle 5.02665 ( 1974) SS BOND : bond 0.01654 ( 42) SS BOND : angle 2.47206 ( 84) covalent geometry : bond 0.01076 (20469) covalent geometry : angle 0.98713 (27807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8233 (tt0) cc_final: 0.7912 (tt0) REVERT: E 268 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6737 (pm20) REVERT: E 426 MET cc_start: 0.7410 (tpp) cc_final: 0.7141 (tpt) REVERT: F 655 LYS cc_start: 0.6500 (ttpt) cc_final: 0.6110 (ttpt) REVERT: L 33 LEU cc_start: 0.5007 (OUTLIER) cc_final: 0.4693 (tp) REVERT: L 85 THR cc_start: 0.3725 (OUTLIER) cc_final: 0.3401 (m) outliers start: 42 outliers final: 22 residues processed: 208 average time/residue: 0.3874 time to fit residues: 116.5535 Evaluate side-chains 194 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 16 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 177 optimal weight: 30.0000 chunk 83 optimal weight: 0.9980 chunk 206 optimal weight: 0.0060 chunk 218 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 246 GLN C 355 ASN D 653 GLN E 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.204105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131704 restraints weight = 20547.018| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.77 r_work: 0.3037 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.059 20598 Z= 0.275 Angle : 0.992 106.100 28152 Z= 0.429 Chirality : 0.046 0.246 3378 Planarity : 0.005 0.080 3429 Dihedral : 11.642 91.811 4370 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 1.74 % Allowed : 13.91 % Favored : 84.35 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2373 helix: 1.77 (0.28), residues: 399 sheet: 0.16 (0.18), residues: 804 loop : -0.99 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.002 0.001 HIS C 374 PHE 0.047 0.002 PHE G 100H TYR 0.012 0.001 TYR C 173 ARG 0.003 0.000 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 45) link_NAG-ASN : angle 2.55993 ( 135) link_BETA1-4 : bond 0.00669 ( 36) link_BETA1-4 : angle 1.34531 ( 108) link_ALPHA1-2 : bond 0.00942 ( 3) link_ALPHA1-2 : angle 1.16619 ( 9) link_ALPHA1-3 : bond 0.01323 ( 3) link_ALPHA1-3 : angle 1.02812 ( 9) hydrogen bonds : bond 0.05040 ( 735) hydrogen bonds : angle 4.98628 ( 1974) SS BOND : bond 0.02213 ( 42) SS BOND : angle 3.11430 ( 84) covalent geometry : bond 0.00962 (20469) covalent geometry : angle 0.96321 (27807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8265 (tt0) cc_final: 0.7949 (tt0) REVERT: C 268 GLU cc_start: 0.7643 (mm-30) cc_final: 0.6623 (pm20) REVERT: C 446 VAL cc_start: 0.8634 (m) cc_final: 0.8428 (t) REVERT: E 268 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6789 (pm20) REVERT: E 426 MET cc_start: 0.7449 (tpp) cc_final: 0.7209 (tpt) REVERT: F 655 LYS cc_start: 0.6619 (ttpt) cc_final: 0.6216 (ttpt) REVERT: L 33 LEU cc_start: 0.5051 (OUTLIER) cc_final: 0.4713 (tp) REVERT: L 85 THR cc_start: 0.3854 (OUTLIER) cc_final: 0.3531 (m) outliers start: 37 outliers final: 27 residues processed: 195 average time/residue: 0.4040 time to fit residues: 112.9238 Evaluate side-chains 197 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 97 optimal weight: 2.9990 chunk 206 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 227 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN E 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.206205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130910 restraints weight = 20747.727| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 4.09 r_work: 0.3085 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.033 20598 Z= 0.236 Angle : 0.912 106.090 28152 Z= 0.389 Chirality : 0.044 0.248 3378 Planarity : 0.005 0.074 3429 Dihedral : 11.207 88.895 4370 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 2.07 % Allowed : 13.67 % Favored : 84.25 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2373 helix: 2.09 (0.29), residues: 399 sheet: 0.18 (0.18), residues: 804 loop : -0.98 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 427 HIS 0.003 0.001 HIS A 374 PHE 0.016 0.001 PHE A 383 TYR 0.014 0.001 TYR C 173 ARG 0.003 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 45) link_NAG-ASN : angle 2.45099 ( 135) link_BETA1-4 : bond 0.00651 ( 36) link_BETA1-4 : angle 1.21824 ( 108) link_ALPHA1-2 : bond 0.00816 ( 3) link_ALPHA1-2 : angle 1.47933 ( 9) link_ALPHA1-3 : bond 0.01296 ( 3) link_ALPHA1-3 : angle 1.55150 ( 9) hydrogen bonds : bond 0.04577 ( 735) hydrogen bonds : angle 4.83984 ( 1974) SS BOND : bond 0.00697 ( 42) SS BOND : angle 2.20267 ( 84) covalent geometry : bond 0.00888 (20469) covalent geometry : angle 0.88892 (27807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8136 (tt0) cc_final: 0.7826 (tt0) REVERT: E 268 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6655 (pm20) REVERT: E 426 MET cc_start: 0.7336 (tpp) cc_final: 0.7097 (tpt) REVERT: K 95 GLN cc_start: 0.5046 (OUTLIER) cc_final: 0.4384 (mt0) REVERT: L 33 LEU cc_start: 0.4878 (OUTLIER) cc_final: 0.4555 (tp) outliers start: 44 outliers final: 29 residues processed: 207 average time/residue: 0.3821 time to fit residues: 114.5586 Evaluate side-chains 200 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 209 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 136 optimal weight: 0.1980 chunk 230 optimal weight: 9.9990 chunk 157 optimal weight: 0.0010 chunk 47 optimal weight: 4.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN E 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.205934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130297 restraints weight = 20796.070| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.21 r_work: 0.3066 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.036 20598 Z= 0.240 Angle : 0.914 106.094 28152 Z= 0.389 Chirality : 0.044 0.249 3378 Planarity : 0.005 0.081 3429 Dihedral : 11.124 88.312 4370 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.95 % Favored : 96.92 % Rotamer: Outliers : 1.93 % Allowed : 13.96 % Favored : 84.11 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2373 helix: 2.10 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 804 loop : -0.99 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS C 374 PHE 0.017 0.001 PHE A 383 TYR 0.012 0.001 TYR C 173 ARG 0.003 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 45) link_NAG-ASN : angle 2.46264 ( 135) link_BETA1-4 : bond 0.00658 ( 36) link_BETA1-4 : angle 1.22600 ( 108) link_ALPHA1-2 : bond 0.00840 ( 3) link_ALPHA1-2 : angle 1.44926 ( 9) link_ALPHA1-3 : bond 0.01292 ( 3) link_ALPHA1-3 : angle 1.51436 ( 9) hydrogen bonds : bond 0.04563 ( 735) hydrogen bonds : angle 4.83475 ( 1974) SS BOND : bond 0.00878 ( 42) SS BOND : angle 2.39990 ( 84) covalent geometry : bond 0.00894 (20469) covalent geometry : angle 0.88984 (27807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8121 (tt0) cc_final: 0.7810 (tt0) REVERT: A 446 VAL cc_start: 0.8595 (m) cc_final: 0.8375 (t) REVERT: E 426 MET cc_start: 0.7335 (tpp) cc_final: 0.7107 (tpt) REVERT: E 430 ILE cc_start: 0.9009 (mt) cc_final: 0.8712 (mm) REVERT: K 95 GLN cc_start: 0.5014 (OUTLIER) cc_final: 0.4357 (mt0) REVERT: L 33 LEU cc_start: 0.4867 (OUTLIER) cc_final: 0.4539 (tp) REVERT: L 85 THR cc_start: 0.3650 (OUTLIER) cc_final: 0.3339 (m) outliers start: 41 outliers final: 34 residues processed: 199 average time/residue: 0.4279 time to fit residues: 123.6591 Evaluate side-chains 207 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 109 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 72 optimal weight: 0.0570 chunk 203 optimal weight: 3.9990 chunk 221 optimal weight: 20.0000 chunk 193 optimal weight: 0.8980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.205738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132359 restraints weight = 20697.411| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.45 r_work: 0.3072 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.046 20598 Z= 0.243 Angle : 0.911 106.088 28152 Z= 0.390 Chirality : 0.044 0.248 3378 Planarity : 0.005 0.091 3429 Dihedral : 10.983 87.272 4370 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.95 % Favored : 96.92 % Rotamer: Outliers : 2.31 % Allowed : 13.58 % Favored : 84.11 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2373 helix: 2.09 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 804 loop : -0.99 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS C 374 PHE 0.017 0.001 PHE A 383 TYR 0.012 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 45) link_NAG-ASN : angle 2.46769 ( 135) link_BETA1-4 : bond 0.00647 ( 36) link_BETA1-4 : angle 1.23918 ( 108) link_ALPHA1-2 : bond 0.00818 ( 3) link_ALPHA1-2 : angle 1.42371 ( 9) link_ALPHA1-3 : bond 0.01288 ( 3) link_ALPHA1-3 : angle 1.49559 ( 9) hydrogen bonds : bond 0.04511 ( 735) hydrogen bonds : angle 4.81553 ( 1974) SS BOND : bond 0.00739 ( 42) SS BOND : angle 2.45903 ( 84) covalent geometry : bond 0.00901 (20469) covalent geometry : angle 0.88574 (27807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8221 (tt0) cc_final: 0.7913 (tt0) REVERT: A 446 VAL cc_start: 0.8610 (m) cc_final: 0.8402 (t) REVERT: E 426 MET cc_start: 0.7373 (tpp) cc_final: 0.7169 (tpt) REVERT: E 430 ILE cc_start: 0.9016 (mt) cc_final: 0.8732 (mm) REVERT: G 112 SER cc_start: 0.1534 (p) cc_final: 0.1294 (m) REVERT: K 95 GLN cc_start: 0.5205 (OUTLIER) cc_final: 0.4528 (mt0) REVERT: L 33 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.4668 (tp) REVERT: L 85 THR cc_start: 0.3822 (OUTLIER) cc_final: 0.3482 (m) outliers start: 49 outliers final: 33 residues processed: 213 average time/residue: 0.3799 time to fit residues: 117.5100 Evaluate side-chains 207 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 134 optimal weight: 0.2980 chunk 157 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN E 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.204645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132452 restraints weight = 20644.429| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.81 r_work: 0.3063 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.046 20598 Z= 0.308 Angle : 0.936 106.087 28152 Z= 0.403 Chirality : 0.044 0.248 3378 Planarity : 0.005 0.091 3429 Dihedral : 10.983 87.272 4370 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.95 % Favored : 96.92 % Rotamer: Outliers : 1.70 % Allowed : 14.19 % Favored : 84.11 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2373 helix: 2.09 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 804 loop : -0.99 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS C 374 PHE 0.017 0.001 PHE A 383 TYR 0.012 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 45) link_NAG-ASN : angle 2.46769 ( 135) link_BETA1-4 : bond 0.00647 ( 36) link_BETA1-4 : angle 1.23917 ( 108) link_ALPHA1-2 : bond 0.00818 ( 3) link_ALPHA1-2 : angle 1.42371 ( 9) link_ALPHA1-3 : bond 0.01288 ( 3) link_ALPHA1-3 : angle 1.49560 ( 9) hydrogen bonds : bond 0.04511 ( 735) hydrogen bonds : angle 4.81553 ( 1974) SS BOND : bond 0.08424 ( 42) SS BOND : angle 4.64379 ( 84) covalent geometry : bond 0.00901 (20469) covalent geometry : angle 0.88573 (27807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8224 (tt0) cc_final: 0.7920 (tt0) REVERT: A 446 VAL cc_start: 0.8605 (m) cc_final: 0.8394 (t) REVERT: E 426 MET cc_start: 0.7385 (tpp) cc_final: 0.7179 (tpt) REVERT: E 430 ILE cc_start: 0.9016 (mt) cc_final: 0.8731 (mm) REVERT: G 112 SER cc_start: 0.1500 (p) cc_final: 0.1262 (m) REVERT: K 95 GLN cc_start: 0.5153 (OUTLIER) cc_final: 0.4482 (mt0) REVERT: L 33 LEU cc_start: 0.4959 (OUTLIER) cc_final: 0.4618 (tp) REVERT: L 85 THR cc_start: 0.3743 (OUTLIER) cc_final: 0.3411 (m) outliers start: 36 outliers final: 33 residues processed: 195 average time/residue: 0.3958 time to fit residues: 110.6238 Evaluate side-chains 205 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 70 optimal weight: 0.6980 chunk 182 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 220 optimal weight: 0.2980 chunk 148 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 122 optimal weight: 0.0980 chunk 203 optimal weight: 0.9990 chunk 194 optimal weight: 30.0000 chunk 195 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.205790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130162 restraints weight = 20791.552| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 4.19 r_work: 0.3069 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.046 20598 Z= 0.308 Angle : 0.936 106.086 28152 Z= 0.403 Chirality : 0.044 0.248 3378 Planarity : 0.005 0.091 3429 Dihedral : 10.983 87.272 4370 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.95 % Favored : 96.92 % Rotamer: Outliers : 1.70 % Allowed : 14.24 % Favored : 84.06 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2373 helix: 2.09 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 804 loop : -0.99 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS C 374 PHE 0.017 0.001 PHE A 383 TYR 0.012 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 45) link_NAG-ASN : angle 2.46768 ( 135) link_BETA1-4 : bond 0.00647 ( 36) link_BETA1-4 : angle 1.23917 ( 108) link_ALPHA1-2 : bond 0.00818 ( 3) link_ALPHA1-2 : angle 1.42372 ( 9) link_ALPHA1-3 : bond 0.01288 ( 3) link_ALPHA1-3 : angle 1.49562 ( 9) hydrogen bonds : bond 0.04511 ( 735) hydrogen bonds : angle 4.81553 ( 1974) SS BOND : bond 0.08418 ( 42) SS BOND : angle 4.64291 ( 84) covalent geometry : bond 0.00901 (20469) covalent geometry : angle 0.88573 (27807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8164 (tt0) cc_final: 0.7853 (tt0) REVERT: A 446 VAL cc_start: 0.8588 (m) cc_final: 0.8374 (t) REVERT: E 426 MET cc_start: 0.7346 (tpp) cc_final: 0.7121 (tpt) REVERT: E 430 ILE cc_start: 0.9004 (mt) cc_final: 0.8709 (mm) REVERT: G 112 SER cc_start: 0.1529 (p) cc_final: 0.1288 (m) REVERT: K 95 GLN cc_start: 0.5067 (OUTLIER) cc_final: 0.4409 (mt0) REVERT: L 33 LEU cc_start: 0.4878 (OUTLIER) cc_final: 0.4550 (tp) REVERT: L 85 THR cc_start: 0.3687 (OUTLIER) cc_final: 0.3359 (m) outliers start: 36 outliers final: 33 residues processed: 194 average time/residue: 0.4095 time to fit residues: 114.4197 Evaluate side-chains 205 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 209 optimal weight: 20.0000 chunk 113 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 197 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.204398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132771 restraints weight = 20614.632| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.93 r_work: 0.3099 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.036 20598 Z= 0.261 Angle : 0.929 106.100 28152 Z= 0.399 Chirality : 0.045 0.249 3378 Planarity : 0.005 0.082 3429 Dihedral : 10.972 87.183 4370 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.91 % Favored : 96.97 % Rotamer: Outliers : 1.93 % Allowed : 14.00 % Favored : 84.06 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2373 helix: 2.08 (0.28), residues: 399 sheet: 0.20 (0.18), residues: 804 loop : -1.00 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS E 216 PHE 0.017 0.001 PHE A 383 TYR 0.057 0.001 TYR G 59 ARG 0.003 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 45) link_NAG-ASN : angle 2.46144 ( 135) link_BETA1-4 : bond 0.00676 ( 36) link_BETA1-4 : angle 1.24651 ( 108) link_ALPHA1-2 : bond 0.00842 ( 3) link_ALPHA1-2 : angle 1.42315 ( 9) link_ALPHA1-3 : bond 0.01282 ( 3) link_ALPHA1-3 : angle 1.49068 ( 9) hydrogen bonds : bond 0.04602 ( 735) hydrogen bonds : angle 4.81606 ( 1974) SS BOND : bond 0.01014 ( 42) SS BOND : angle 3.63014 ( 84) covalent geometry : bond 0.00934 (20469) covalent geometry : angle 0.89268 (27807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8233 (tt0) cc_final: 0.7931 (tt0) REVERT: A 446 VAL cc_start: 0.8628 (m) cc_final: 0.8420 (t) REVERT: E 426 MET cc_start: 0.7393 (tpp) cc_final: 0.7182 (tpt) REVERT: E 430 ILE cc_start: 0.9020 (mt) cc_final: 0.8739 (mm) REVERT: G 112 SER cc_start: 0.1568 (p) cc_final: 0.1329 (m) REVERT: K 95 GLN cc_start: 0.5181 (OUTLIER) cc_final: 0.4509 (mt0) REVERT: L 33 LEU cc_start: 0.5029 (OUTLIER) cc_final: 0.4681 (tp) REVERT: L 85 THR cc_start: 0.3859 (OUTLIER) cc_final: 0.3515 (m) outliers start: 41 outliers final: 35 residues processed: 199 average time/residue: 0.3956 time to fit residues: 113.6006 Evaluate side-chains 206 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 235 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.204288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.132146 restraints weight = 20667.032| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.99 r_work: 0.3111 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.036 20598 Z= 0.344 Angle : 0.948 106.100 28152 Z= 0.410 Chirality : 0.045 0.249 3378 Planarity : 0.005 0.082 3429 Dihedral : 10.972 87.183 4370 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.91 % Favored : 96.97 % Rotamer: Outliers : 1.79 % Allowed : 14.19 % Favored : 84.02 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2373 helix: 2.08 (0.28), residues: 399 sheet: 0.20 (0.18), residues: 804 loop : -1.00 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS E 216 PHE 0.017 0.001 PHE A 383 TYR 0.057 0.001 TYR G 59 ARG 0.003 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 45) link_NAG-ASN : angle 2.46144 ( 135) link_BETA1-4 : bond 0.00676 ( 36) link_BETA1-4 : angle 1.24651 ( 108) link_ALPHA1-2 : bond 0.00842 ( 3) link_ALPHA1-2 : angle 1.42315 ( 9) link_ALPHA1-3 : bond 0.01282 ( 3) link_ALPHA1-3 : angle 1.49068 ( 9) hydrogen bonds : bond 0.04602 ( 735) hydrogen bonds : angle 4.81606 ( 1974) SS BOND : bond 0.09959 ( 42) SS BOND : angle 5.01895 ( 84) covalent geometry : bond 0.00934 (20469) covalent geometry : angle 0.89268 (27807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8215 (tt0) cc_final: 0.7909 (tt0) REVERT: A 446 VAL cc_start: 0.8622 (m) cc_final: 0.8414 (t) REVERT: E 426 MET cc_start: 0.7375 (tpp) cc_final: 0.7161 (tpt) REVERT: E 430 ILE cc_start: 0.9016 (mt) cc_final: 0.8732 (mm) REVERT: G 112 SER cc_start: 0.1592 (p) cc_final: 0.1351 (m) REVERT: K 95 GLN cc_start: 0.5190 (OUTLIER) cc_final: 0.4512 (mt0) REVERT: L 33 LEU cc_start: 0.5035 (OUTLIER) cc_final: 0.4686 (tp) REVERT: L 85 THR cc_start: 0.3881 (OUTLIER) cc_final: 0.3535 (m) outliers start: 38 outliers final: 35 residues processed: 195 average time/residue: 0.4061 time to fit residues: 113.5991 Evaluate side-chains 206 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 107 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 233 optimal weight: 50.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.204288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131974 restraints weight = 20715.115| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 4.22 r_work: 0.3068 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.036 20598 Z= 0.344 Angle : 0.948 106.100 28152 Z= 0.410 Chirality : 0.045 0.249 3378 Planarity : 0.005 0.082 3429 Dihedral : 10.972 87.183 4370 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.91 % Favored : 96.97 % Rotamer: Outliers : 1.79 % Allowed : 14.19 % Favored : 84.02 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2373 helix: 2.08 (0.28), residues: 399 sheet: 0.20 (0.18), residues: 804 loop : -1.00 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS E 216 PHE 0.017 0.001 PHE A 383 TYR 0.057 0.001 TYR G 59 ARG 0.003 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 45) link_NAG-ASN : angle 2.46144 ( 135) link_BETA1-4 : bond 0.00676 ( 36) link_BETA1-4 : angle 1.24651 ( 108) link_ALPHA1-2 : bond 0.00842 ( 3) link_ALPHA1-2 : angle 1.42315 ( 9) link_ALPHA1-3 : bond 0.01282 ( 3) link_ALPHA1-3 : angle 1.49068 ( 9) hydrogen bonds : bond 0.04602 ( 735) hydrogen bonds : angle 4.81606 ( 1974) SS BOND : bond 0.09959 ( 42) SS BOND : angle 5.01895 ( 84) covalent geometry : bond 0.00934 (20469) covalent geometry : angle 0.89268 (27807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11979.99 seconds wall clock time: 207 minutes 48.86 seconds (12468.86 seconds total)