Starting phenix.real_space_refine on Tue Jun 17 14:31:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tkc_41346/06_2025/8tkc_41346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tkc_41346/06_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_41346/06_2025/8tkc_41346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tkc_41346/06_2025/8tkc_41346.map" model { file = "/net/cci-nas-00/data/ceres_data/8tkc_41346/06_2025/8tkc_41346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tkc_41346/06_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-5710/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: 12.88, per 1000 atoms: 0.64 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: 5.24 Conformation dependent library (CDL) restraints added in 2.3 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: 2.46 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: 7.03 Time building geometry restraints manager: 6.20 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: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 46.150 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.140 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.300 ------------------------------------------------------------------------------- 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 : 2.064 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: 0.4405 time to fit residues: 114.5462 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 : 2.006 ------------------------------------------------------------------------------- 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 = 0.130493 restraints weight = 20798.785| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.69 r_work: 0.3071 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 1.011 106.098 28152 Z= 0.441 Chirality : 0.051 0.252 3378 Planarity : 0.005 0.083 3429 Dihedral : 11.756 91.997 4377 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.04 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 2.60992 ( 135) link_BETA1-4 : bond 0.00953 ( 36) link_BETA1-4 : angle 1.46434 ( 108) link_ALPHA1-2 : bond 0.00592 ( 3) link_ALPHA1-2 : angle 1.55197 ( 9) link_ALPHA1-3 : bond 0.01641 ( 3) link_ALPHA1-3 : angle 0.79269 ( 9) hydrogen bonds : bond 0.05467 ( 735) hydrogen bonds : angle 5.02666 ( 1974) SS BOND : bond 0.01655 ( 42) SS BOND : angle 2.47213 ( 84) covalent geometry : bond 0.01076 (20469) covalent geometry : angle 0.98714 (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 : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8247 (tt0) cc_final: 0.7928 (tt0) REVERT: E 268 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6742 (pm20) REVERT: E 426 MET cc_start: 0.7425 (tpp) cc_final: 0.7164 (tpt) REVERT: F 655 LYS cc_start: 0.6526 (ttpt) cc_final: 0.6136 (ttpt) REVERT: L 33 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4693 (tp) REVERT: L 85 THR cc_start: 0.3729 (OUTLIER) cc_final: 0.3403 (m) outliers start: 42 outliers final: 22 residues processed: 208 average time/residue: 0.5138 time to fit residues: 156.5800 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 : 1.925 ------------------------------------------------------------------------------- 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: 1.9990 chunk 69 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 177 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 206 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 355 ASN D 653 GLN E 355 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.203009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129844 restraints weight = 20504.898| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.83 r_work: 0.3020 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.021 20598 Z= 0.258 Angle : 0.923 105.858 28152 Z= 0.394 Chirality : 0.045 0.250 3378 Planarity : 0.005 0.087 3429 Dihedral : 10.639 85.012 4370 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 2.50 % Allowed : 13.30 % Favored : 84.21 % 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: -0.13 (0.17), residues: 2373 helix: 1.92 (0.28), residues: 399 sheet: 0.21 (0.18), residues: 804 loop : -1.01 (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 A 374 PHE 0.019 0.002 PHE A 383 TYR 0.015 0.001 TYR C 173 ARG 0.003 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 45) link_NAG-ASN : angle 2.57070 ( 135) link_BETA1-4 : bond 0.00636 ( 36) link_BETA1-4 : angle 1.27845 ( 108) link_ALPHA1-2 : bond 0.00835 ( 3) link_ALPHA1-2 : angle 1.48244 ( 9) link_ALPHA1-3 : bond 0.01255 ( 3) link_ALPHA1-3 : angle 1.49025 ( 9) hydrogen bonds : bond 0.04938 ( 735) hydrogen bonds : angle 4.84518 ( 1974) SS BOND : bond 0.00606 ( 42) SS BOND : angle 2.06462 ( 84) covalent geometry : bond 0.00927 (20469) covalent geometry : angle 0.89941 (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 233 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 180 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8244 (tt0) cc_final: 0.7946 (tt0) REVERT: C 268 GLU cc_start: 0.7686 (mm-30) cc_final: 0.6654 (pm20) REVERT: E 426 MET cc_start: 0.7512 (tpp) cc_final: 0.7274 (tpt) REVERT: E 446 VAL cc_start: 0.8621 (m) cc_final: 0.8391 (t) REVERT: K 95 GLN cc_start: 0.5264 (OUTLIER) cc_final: 0.4604 (mt0) REVERT: L 33 LEU cc_start: 0.5036 (OUTLIER) cc_final: 0.4687 (tp) outliers start: 53 outliers final: 29 residues processed: 221 average time/residue: 0.3784 time to fit residues: 121.8012 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 : 2.075 ------------------------------------------------------------------------------- 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 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 325 ASP Chi-restraints excluded: chain C residue 355 ASN 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 496 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 97 optimal weight: 2.9990 chunk 206 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 0.0470 chunk 163 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 63 optimal weight: 0.0370 chunk 150 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 462 ASN C 462 ASN D 653 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.205515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133419 restraints weight = 20675.526| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.58 r_work: 0.3104 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 20598 Z= 0.108 Angle : 0.570 14.307 28152 Z= 0.285 Chirality : 0.043 0.255 3378 Planarity : 0.005 0.108 3429 Dihedral : 8.411 66.289 4370 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.82 % Favored : 97.05 % Rotamer: Outliers : 2.07 % Allowed : 14.00 % Favored : 83.92 % Cbeta Deviations : 0.00 % 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: 0.02 (0.17), residues: 2373 helix: 2.21 (0.28), residues: 399 sheet: 0.43 (0.19), residues: 750 loop : -1.02 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 427 HIS 0.002 0.000 HIS A 216 PHE 0.012 0.001 PHE A 383 TYR 0.016 0.001 TYR C 173 ARG 0.003 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 45) link_NAG-ASN : angle 2.38669 ( 135) link_BETA1-4 : bond 0.00534 ( 36) link_BETA1-4 : angle 1.32208 ( 108) link_ALPHA1-2 : bond 0.00603 ( 3) link_ALPHA1-2 : angle 1.45934 ( 9) link_ALPHA1-3 : bond 0.01229 ( 3) link_ALPHA1-3 : angle 1.58456 ( 9) hydrogen bonds : bond 0.03748 ( 735) hydrogen bonds : angle 4.61167 ( 1974) SS BOND : bond 0.00467 ( 42) SS BOND : angle 1.71949 ( 84) covalent geometry : bond 0.00247 (20469) covalent geometry : angle 0.53256 (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 218 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8245 (tt0) cc_final: 0.7955 (tt0) REVERT: A 430 ILE cc_start: 0.9096 (mt) cc_final: 0.8824 (mm) REVERT: E 357 THR cc_start: 0.7763 (m) cc_final: 0.7474 (t) REVERT: K 95 GLN cc_start: 0.5202 (OUTLIER) cc_final: 0.4520 (mt0) REVERT: L 33 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4675 (tp) outliers start: 44 outliers final: 25 residues processed: 208 average time/residue: 0.3768 time to fit residues: 113.6513 Evaluate side-chains 191 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 325 ASP Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR 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 D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE 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 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 88 CYS 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: 0.9990 chunk 79 optimal weight: 2.9990 chunk 209 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 224 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 230 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 137 ASN C 355 ASN D 607 ASN D 653 GLN E 289 ASN E 462 ASN L 38 GLN L 92 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.197713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123588 restraints weight = 20617.318| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 4.01 r_work: 0.2960 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 20598 Z= 0.253 Angle : 0.782 13.627 28152 Z= 0.377 Chirality : 0.050 0.278 3378 Planarity : 0.005 0.068 3429 Dihedral : 7.470 59.862 4368 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.71 % Favored : 96.17 % Rotamer: Outliers : 3.06 % Allowed : 13.30 % Favored : 83.64 % Cbeta Deviations : 0.00 % 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: -0.20 (0.17), residues: 2373 helix: 1.78 (0.28), residues: 402 sheet: 0.48 (0.19), residues: 753 loop : -1.22 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 103 HIS 0.004 0.001 HIS A 249 PHE 0.026 0.002 PHE A 383 TYR 0.016 0.002 TYR C 173 ARG 0.003 0.000 ARG E 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 45) link_NAG-ASN : angle 3.05347 ( 135) link_BETA1-4 : bond 0.00657 ( 36) link_BETA1-4 : angle 1.57853 ( 108) link_ALPHA1-2 : bond 0.00790 ( 3) link_ALPHA1-2 : angle 1.30876 ( 9) link_ALPHA1-3 : bond 0.01125 ( 3) link_ALPHA1-3 : angle 1.16710 ( 9) hydrogen bonds : bond 0.06372 ( 735) hydrogen bonds : angle 4.95686 ( 1974) SS BOND : bond 0.00630 ( 42) SS BOND : angle 2.50594 ( 84) covalent geometry : bond 0.00650 (20469) covalent geometry : angle 0.73768 (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 229 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 164 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7825 (t) cc_final: 0.7474 (t) REVERT: A 114 GLN cc_start: 0.8218 (tt0) cc_final: 0.7890 (tt0) REVERT: A 129 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8712 (mt) REVERT: C 136 ASN cc_start: 0.6691 (m-40) cc_final: 0.5836 (p0) REVERT: E 215 ILE cc_start: 0.9089 (mt) cc_final: 0.8646 (pt) REVERT: I 95 GLN cc_start: 0.5888 (OUTLIER) cc_final: 0.5214 (mt0) REVERT: J 32 ASP cc_start: 0.5135 (OUTLIER) cc_final: 0.4453 (p0) REVERT: K 95 GLN cc_start: 0.5677 (OUTLIER) cc_final: 0.5005 (mt0) REVERT: L 32 ASP cc_start: 0.4739 (OUTLIER) cc_final: 0.4394 (p0) REVERT: L 85 THR cc_start: 0.4071 (OUTLIER) cc_final: 0.3724 (m) outliers start: 65 outliers final: 39 residues processed: 216 average time/residue: 0.3690 time to fit residues: 118.4858 Evaluate side-chains 205 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR 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 341 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS 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 67 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 442 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 88 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 32 ASP 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 32 ASP 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: 0.9990 chunk 65 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 chunk 213 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 221 optimal weight: 0.0770 chunk 193 optimal weight: 0.9980 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 575 GLN C 355 ASN D 575 GLN E 136 ASN E 355 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.201581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.130817 restraints weight = 20636.360| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.40 r_work: 0.2992 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20598 Z= 0.120 Angle : 0.603 10.325 28152 Z= 0.298 Chirality : 0.044 0.279 3378 Planarity : 0.004 0.067 3429 Dihedral : 6.386 57.287 4368 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.16 % Favored : 96.71 % Rotamer: Outliers : 2.36 % Allowed : 14.71 % Favored : 82.93 % Cbeta Deviations : 0.00 % 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: -0.04 (0.17), residues: 2373 helix: 2.06 (0.28), residues: 399 sheet: 0.51 (0.19), residues: 756 loop : -1.13 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 427 HIS 0.002 0.001 HIS E 216 PHE 0.016 0.001 PHE A 383 TYR 0.017 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 45) link_NAG-ASN : angle 2.69812 ( 135) link_BETA1-4 : bond 0.00520 ( 36) link_BETA1-4 : angle 1.33974 ( 108) link_ALPHA1-2 : bond 0.00539 ( 3) link_ALPHA1-2 : angle 1.48187 ( 9) link_ALPHA1-3 : bond 0.01204 ( 3) link_ALPHA1-3 : angle 1.32842 ( 9) hydrogen bonds : bond 0.04367 ( 735) hydrogen bonds : angle 4.66201 ( 1974) SS BOND : bond 0.00508 ( 42) SS BOND : angle 2.07062 ( 84) covalent geometry : bond 0.00286 (20469) covalent geometry : angle 0.55808 (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 216 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7843 (t) cc_final: 0.7474 (t) REVERT: A 114 GLN cc_start: 0.8259 (tt0) cc_final: 0.7956 (tt0) REVERT: A 136 ASN cc_start: 0.6784 (m-40) cc_final: 0.5738 (p0) REVERT: A 426 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7591 (tpt) REVERT: A 430 ILE cc_start: 0.9112 (mt) cc_final: 0.8841 (mm) REVERT: C 426 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7385 (tpt) REVERT: E 136 ASN cc_start: 0.6855 (OUTLIER) cc_final: 0.6448 (m110) REVERT: E 215 ILE cc_start: 0.9115 (mt) cc_final: 0.8697 (pt) REVERT: E 357 THR cc_start: 0.8094 (t) cc_final: 0.7893 (t) REVERT: I 95 GLN cc_start: 0.5766 (OUTLIER) cc_final: 0.5099 (mt0) REVERT: K 95 GLN cc_start: 0.5520 (OUTLIER) cc_final: 0.4873 (mt0) REVERT: L 85 THR cc_start: 0.4066 (OUTLIER) cc_final: 0.3728 (m) outliers start: 50 outliers final: 30 residues processed: 203 average time/residue: 0.3695 time to fit residues: 111.3921 Evaluate side-chains 196 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 2.169 ------------------------------------------------------------------------------- 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 325 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 501 CYS 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 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 136 ASN 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 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 95 GLN 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 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 134 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 155 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN C 355 ASN D 607 ASN D 653 GLN E 289 ASN E 355 ASN H 38 GLN H 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.198934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127458 restraints weight = 20586.358| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.41 r_work: 0.3034 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20598 Z= 0.198 Angle : 0.697 14.313 28152 Z= 0.336 Chirality : 0.047 0.288 3378 Planarity : 0.005 0.067 3429 Dihedral : 6.138 55.213 4368 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.50 % Favored : 96.38 % Rotamer: Outliers : 2.50 % Allowed : 14.95 % Favored : 82.56 % Cbeta Deviations : 0.00 % 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: -0.11 (0.17), residues: 2373 helix: 1.92 (0.28), residues: 399 sheet: 0.51 (0.19), residues: 753 loop : -1.17 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 427 HIS 0.003 0.001 HIS A 249 PHE 0.021 0.002 PHE E 383 TYR 0.020 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 45) link_NAG-ASN : angle 2.79253 ( 135) link_BETA1-4 : bond 0.00586 ( 36) link_BETA1-4 : angle 1.41145 ( 108) link_ALPHA1-2 : bond 0.00620 ( 3) link_ALPHA1-2 : angle 1.41586 ( 9) link_ALPHA1-3 : bond 0.01077 ( 3) link_ALPHA1-3 : angle 1.19024 ( 9) hydrogen bonds : bond 0.05293 ( 735) hydrogen bonds : angle 4.77047 ( 1974) SS BOND : bond 0.00566 ( 42) SS BOND : angle 2.35919 ( 84) covalent geometry : bond 0.00505 (20469) covalent geometry : angle 0.65436 (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 213 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7821 (t) cc_final: 0.7500 (t) REVERT: A 114 GLN cc_start: 0.8262 (tt0) cc_final: 0.7954 (tt0) REVERT: C 136 ASN cc_start: 0.6707 (m-40) cc_final: 0.5861 (p0) REVERT: E 215 ILE cc_start: 0.9126 (mt) cc_final: 0.8707 (pt) REVERT: I 95 GLN cc_start: 0.5889 (OUTLIER) cc_final: 0.5222 (mt0) REVERT: K 95 GLN cc_start: 0.5536 (OUTLIER) cc_final: 0.4885 (mt0) REVERT: L 85 THR cc_start: 0.4037 (OUTLIER) cc_final: 0.3693 (m) outliers start: 53 outliers final: 36 residues processed: 201 average time/residue: 0.5113 time to fit residues: 154.7835 Evaluate side-chains 200 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 2.690 ------------------------------------------------------------------------------- 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 325 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR 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 325 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 613 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 67 ASN 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 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 H residue 88 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 95 GLN 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: 0.9990 chunk 182 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 220 optimal weight: 0.1980 chunk 148 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 355 ASN E 355 ASN F 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.201597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.129963 restraints weight = 20663.097| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.41 r_work: 0.2946 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20598 Z= 0.154 Angle : 0.631 11.596 28152 Z= 0.310 Chirality : 0.045 0.295 3378 Planarity : 0.004 0.066 3429 Dihedral : 5.458 50.675 4368 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.37 % Favored : 96.50 % Rotamer: Outliers : 2.78 % Allowed : 14.76 % Favored : 82.46 % Cbeta Deviations : 0.00 % 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: -0.06 (0.17), residues: 2373 helix: 1.96 (0.28), residues: 399 sheet: 0.57 (0.19), residues: 753 loop : -1.16 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS A 249 PHE 0.017 0.001 PHE E 383 TYR 0.020 0.001 TYR C 173 ARG 0.005 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 45) link_NAG-ASN : angle 2.72063 ( 135) link_BETA1-4 : bond 0.00554 ( 36) link_BETA1-4 : angle 1.34760 ( 108) link_ALPHA1-2 : bond 0.00537 ( 3) link_ALPHA1-2 : angle 1.48071 ( 9) link_ALPHA1-3 : bond 0.01154 ( 3) link_ALPHA1-3 : angle 1.19680 ( 9) hydrogen bonds : bond 0.04716 ( 735) hydrogen bonds : angle 4.65632 ( 1974) SS BOND : bond 0.00549 ( 42) SS BOND : angle 2.09686 ( 84) covalent geometry : bond 0.00386 (20469) covalent geometry : angle 0.58812 (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 225 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 166 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8211 (tt0) cc_final: 0.7915 (tt0) REVERT: C 136 ASN cc_start: 0.6738 (m-40) cc_final: 0.5897 (p0) REVERT: C 151 ARG cc_start: 0.8360 (mtp-110) cc_final: 0.7774 (mtt-85) REVERT: C 426 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7519 (tpp) REVERT: E 153 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7316 (mm-30) REVERT: E 215 ILE cc_start: 0.9121 (mt) cc_final: 0.8720 (pt) REVERT: I 95 GLN cc_start: 0.5820 (OUTLIER) cc_final: 0.5186 (mt0) REVERT: K 95 GLN cc_start: 0.5508 (OUTLIER) cc_final: 0.4924 (mt0) REVERT: L 85 THR cc_start: 0.4109 (OUTLIER) cc_final: 0.3800 (m) outliers start: 59 outliers final: 42 residues processed: 211 average time/residue: 0.5909 time to fit residues: 195.4043 Evaluate side-chains 206 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 2.927 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR 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 277 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 442 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 88 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 95 GLN 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: 7.9990 chunk 113 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 199 optimal weight: 0.2980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 355 ASN D 653 GLN E 136 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 = 0.4168 r_free = 0.4168 target = 0.200070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129546 restraints weight = 20513.246| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.41 r_work: 0.2928 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20598 Z= 0.153 Angle : 0.645 15.234 28152 Z= 0.314 Chirality : 0.045 0.295 3378 Planarity : 0.004 0.066 3429 Dihedral : 5.307 49.108 4368 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 2.59 % Allowed : 14.80 % Favored : 82.60 % Cbeta Deviations : 0.00 % 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: -0.04 (0.17), residues: 2373 helix: 1.98 (0.28), residues: 399 sheet: 0.59 (0.19), residues: 753 loop : -1.15 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 427 HIS 0.003 0.001 HIS C 216 PHE 0.018 0.001 PHE E 383 TYR 0.021 0.001 TYR C 173 ARG 0.005 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 45) link_NAG-ASN : angle 2.70967 ( 135) link_BETA1-4 : bond 0.00541 ( 36) link_BETA1-4 : angle 1.33918 ( 108) link_ALPHA1-2 : bond 0.00529 ( 3) link_ALPHA1-2 : angle 1.48010 ( 9) link_ALPHA1-3 : bond 0.01103 ( 3) link_ALPHA1-3 : angle 1.16083 ( 9) hydrogen bonds : bond 0.04741 ( 735) hydrogen bonds : angle 4.64678 ( 1974) SS BOND : bond 0.00560 ( 42) SS BOND : angle 2.18650 ( 84) covalent geometry : bond 0.00385 (20469) covalent geometry : angle 0.60210 (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 214 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8233 (tt0) cc_final: 0.7925 (tt0) REVERT: C 136 ASN cc_start: 0.6771 (m-40) cc_final: 0.5930 (p0) REVERT: E 136 ASN cc_start: 0.6890 (m-40) cc_final: 0.5969 (p0) REVERT: E 153 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: E 215 ILE cc_start: 0.9131 (mt) cc_final: 0.8729 (pt) REVERT: I 95 GLN cc_start: 0.5798 (OUTLIER) cc_final: 0.5186 (mt0) REVERT: K 95 GLN cc_start: 0.5512 (OUTLIER) cc_final: 0.4932 (mt0) REVERT: L 85 THR cc_start: 0.4088 (OUTLIER) cc_final: 0.3784 (m) outliers start: 55 outliers final: 48 residues processed: 199 average time/residue: 0.5558 time to fit residues: 166.7043 Evaluate side-chains 209 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 157 time to evaluate : 4.492 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR 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 277 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 457 ASP 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 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 95 GLN 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: 0.9980 chunk 78 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 161 optimal weight: 0.0670 chunk 10 optimal weight: 0.0870 chunk 85 optimal weight: 0.5980 chunk 235 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 355 ASN E 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.202438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131301 restraints weight = 20470.067| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.25 r_work: 0.3064 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20598 Z= 0.110 Angle : 0.575 11.412 28152 Z= 0.286 Chirality : 0.043 0.293 3378 Planarity : 0.004 0.065 3429 Dihedral : 4.909 44.565 4368 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.12 % Favored : 96.76 % Rotamer: Outliers : 2.17 % Allowed : 15.42 % Favored : 82.41 % Cbeta Deviations : 0.00 % 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: 2.12 (0.28), residues: 399 sheet: 0.63 (0.19), residues: 765 loop : -1.06 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 427 HIS 0.002 0.001 HIS C 216 PHE 0.014 0.001 PHE C 353 TYR 0.021 0.001 TYR C 173 ARG 0.006 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 45) link_NAG-ASN : angle 2.57074 ( 135) link_BETA1-4 : bond 0.00514 ( 36) link_BETA1-4 : angle 1.26399 ( 108) link_ALPHA1-2 : bond 0.00434 ( 3) link_ALPHA1-2 : angle 1.49730 ( 9) link_ALPHA1-3 : bond 0.01097 ( 3) link_ALPHA1-3 : angle 1.15651 ( 9) hydrogen bonds : bond 0.03987 ( 735) hydrogen bonds : angle 4.50615 ( 1974) SS BOND : bond 0.00456 ( 42) SS BOND : angle 1.91603 ( 84) covalent geometry : bond 0.00263 (20469) covalent geometry : angle 0.53321 (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 215 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8172 (tt0) cc_final: 0.7860 (tt0) REVERT: A 426 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7430 (tpt) REVERT: A 430 ILE cc_start: 0.9106 (mt) cc_final: 0.8852 (mm) REVERT: C 136 ASN cc_start: 0.6750 (m-40) cc_final: 0.5897 (p0) REVERT: C 151 ARG cc_start: 0.8305 (mtp-110) cc_final: 0.7690 (mtp85) REVERT: C 502 LYS cc_start: 0.8385 (ptmm) cc_final: 0.8078 (tttp) REVERT: E 136 ASN cc_start: 0.6868 (m-40) cc_final: 0.5929 (p0) REVERT: E 153 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7285 (mm-30) REVERT: E 215 ILE cc_start: 0.9113 (mt) cc_final: 0.8717 (pt) REVERT: I 95 GLN cc_start: 0.5764 (OUTLIER) cc_final: 0.5205 (mt0) REVERT: K 95 GLN cc_start: 0.5450 (OUTLIER) cc_final: 0.4936 (mt0) REVERT: L 85 THR cc_start: 0.4117 (OUTLIER) cc_final: 0.3797 (m) outliers start: 46 outliers final: 38 residues processed: 203 average time/residue: 0.4019 time to fit residues: 119.0363 Evaluate side-chains 204 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 325 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR 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 325 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 184 ILE 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 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 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 95 GLN 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: 1.9990 chunk 88 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 233 optimal weight: 30.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 289 ASN C 355 ASN E 137 ASN E 246 GLN E 355 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.200166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128505 restraints weight = 20642.877| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.84 r_work: 0.2935 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20598 Z= 0.156 Angle : 0.638 12.571 28152 Z= 0.312 Chirality : 0.045 0.300 3378 Planarity : 0.004 0.065 3429 Dihedral : 4.893 42.648 4368 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.33 % Favored : 96.54 % Rotamer: Outliers : 2.69 % Allowed : 14.76 % Favored : 82.56 % Cbeta Deviations : 0.00 % 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: 0.04 (0.17), residues: 2373 helix: 2.04 (0.28), residues: 399 sheet: 0.67 (0.19), residues: 753 loop : -1.11 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 427 HIS 0.003 0.001 HIS C 216 PHE 0.019 0.001 PHE A 383 TYR 0.021 0.001 TYR C 173 ARG 0.006 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 45) link_NAG-ASN : angle 2.65045 ( 135) link_BETA1-4 : bond 0.00544 ( 36) link_BETA1-4 : angle 1.29225 ( 108) link_ALPHA1-2 : bond 0.00492 ( 3) link_ALPHA1-2 : angle 1.46291 ( 9) link_ALPHA1-3 : bond 0.01059 ( 3) link_ALPHA1-3 : angle 1.10078 ( 9) hydrogen bonds : bond 0.04690 ( 735) hydrogen bonds : angle 4.59116 ( 1974) SS BOND : bond 0.00610 ( 42) SS BOND : angle 2.18425 ( 84) covalent geometry : bond 0.00391 (20469) covalent geometry : angle 0.59681 (27807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14275.80 seconds wall clock time: 259 minutes 21.85 seconds (15561.85 seconds total)