Starting phenix.real_space_refine on Thu Mar 5 14:57:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uot_26653/03_2026/7uot_26653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uot_26653/03_2026/7uot_26653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uot_26653/03_2026/7uot_26653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uot_26653/03_2026/7uot_26653.map" model { file = "/net/cci-nas-00/data/ceres_data/7uot_26653/03_2026/7uot_26653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uot_26653/03_2026/7uot_26653.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7980 atoms to isotropic. 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 112 5.16 5 C 10505 2.51 5 N 2677 2.21 5 O 3540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16834 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1521 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "a" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1224 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "T" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "S" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1521 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "b" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1224 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "P" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "O" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "C" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1521 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "c" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1224 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "R" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "Q" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "H" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1048 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "L" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 794 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "k" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "l" 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: "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: 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: "q" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.79, per 1000 atoms: 0.23 Number of scatterers: 16834 At special positions: 0 Unit cell: (138.6, 147.84, 124.74, 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 112 16.00 O 3540 8.00 N 2677 7.00 C 10505 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN g 4 " - " MAN g 5 " " MAN r 4 " - " MAN r 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA M 3 " - " MAN M 4 " " BMA V 3 " - " MAN V 4 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA M 3 " - " MAN M 6 " " BMA V 3 " - " MAN V 5 " " BMA Z 3 " - " MAN Z 4 " " BMA g 3 " - " MAN g 6 " " BMA j 3 " - " MAN j 5 " " BMA q 3 " - " MAN q 5 " " BMA r 3 " - " MAN r 6 " " BMA u 3 " - " MAN u 5 " BETA1-3 " NAG f 1 " - " FUC f 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " 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 u 2 " - " BMA u 3 " BETA1-6 " NAG G 1 " - " FUC G 4 " " NAG I 1 " - " FUC I 6 " " NAG U 1 " - " FUC U 3 " " NAG V 1 " - " FUC V 6 " " NAG X 1 " - " FUC X 4 " " NAG i 1 " - " FUC i 3 " " NAG j 1 " - " FUC j 6 " " NAG k 1 " - " FUC k 4 " " NAG q 1 " - " FUC q 6 " " NAG t 1 " - " FUC t 3 " " NAG u 1 " - " FUC u 6 " NAG-ASN " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 99 " " NAG G 1 " - " ASN A 109 " " NAG I 1 " - " ASN A 119 " " NAG J 1 " - " ASN A 167 " " NAG K 1 " - " ASN A 224 " " NAG M 1 " - " ASN a 365 " " NAG N 1 " - " ASN a 373 " " NAG U 1 " - " ASN a 390 " " NAG V 1 " - " ASN a 395 " " NAG W 1 " - " ASN B 89 " " NAG X 1 " - " ASN B 109 " " NAG Y 1 " - " ASN B 167 " " NAG Z 1 " - " ASN B 79 " " NAG d 1 " - " ASN B 99 " " NAG e 1 " - " ASN B 224 " " NAG f 1 " - " ASN B 119 " " NAG g 1 " - " ASN b 365 " " NAG h 1 " - " ASN b 373 " " NAG i 1 " - " ASN b 390 " " NAG j 1 " - " ASN b 395 " " NAG k 1 " - " ASN C 109 " " NAG l 1 " - " ASN C 79 " " NAG m 1 " - " ASN C 89 " " NAG n 1 " - " ASN C 99 " " NAG o 1 " - " ASN C 167 " " NAG p 1 " - " ASN C 224 " " NAG q 1 " - " ASN C 119 " " NAG r 1 " - " ASN c 365 " " NAG s 1 " - " ASN c 373 " " NAG t 1 " - " ASN c 390 " " NAG u 1 " - " ASN c 395 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 601.3 milliseconds 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3610 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 35 sheets defined 24.3% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.806A pdb=" N GLY A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 198 through 203 removed outlier: 4.102A pdb=" N ILE A 201 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'a' and resid 294 through 300 removed outlier: 3.911A pdb=" N LYS a 300 " --> pdb=" O THR a 296 " (cutoff:3.500A) Processing helix chain 'a' and resid 301 through 303 No H-bonds generated for 'chain 'a' and resid 301 through 303' Processing helix chain 'a' and resid 307 through 326 removed outlier: 3.608A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 334 through 341 Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.875A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 416 Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.760A pdb=" N PHE T 83 " --> pdb=" O SER T 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.936A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.718A pdb=" N LYS B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.636A pdb=" N ILE B 201 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP B 204 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 4.214A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 300 removed outlier: 3.808A pdb=" N LYS b 300 " --> pdb=" O THR b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 301 through 303 No H-bonds generated for 'chain 'b' and resid 301 through 303' Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 334 through 340 Processing helix chain 'b' and resid 346 through 360 removed outlier: 3.843A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 416 removed outlier: 3.563A pdb=" N GLN b 416 " --> pdb=" O THR b 412 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.662A pdb=" N TYR O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.704A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.839A pdb=" N ASP C 204 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 334 through 341 Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.899A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 416 removed outlier: 3.660A pdb=" N GLN c 416 " --> pdb=" O THR c 412 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.509A pdb=" N TYR Q 32 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 65 removed outlier: 4.005A pdb=" N GLN Q 65 " --> pdb=" O GLN Q 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 62 through 65' Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.928A pdb=" N THR Q 91 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.578A pdb=" N GLY H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.586A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'L' and resid 26 through 29 Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.507A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 156 removed outlier: 5.650A pdb=" N THR A 87 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG A 235 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AA4, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'T' and resid 4 through 5 removed outlier: 12.301A pdb=" N CYS T 23 " --> pdb=" O THR T 74 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N THR T 74 " --> pdb=" O CYS T 23 " (cutoff:3.500A) removed outlier: 11.951A pdb=" N ALA T 25 " --> pdb=" O THR T 72 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N THR T 72 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 11.249A pdb=" N GLN T 27 " --> pdb=" O GLU T 70 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLU T 70 " --> pdb=" O GLN T 27 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY T 68 " --> pdb=" O VAL T 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 53 through 54 removed outlier: 6.438A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER T 97 " --> pdb=" O GLN T 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'T' and resid 53 through 54 removed outlier: 6.438A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 4 through 5 removed outlier: 3.534A pdb=" N VAL S 5 " --> pdb=" O LYS S 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 11 removed outlier: 3.524A pdb=" N THR S 125 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TRP S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 11 removed outlier: 3.524A pdb=" N THR S 125 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL S 117 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AB3, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.563A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB5, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AB6, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.615A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 10 through 11 removed outlier: 3.821A pdb=" N SER P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AC1, first strand: chain 'O' and resid 10 through 11 removed outlier: 3.858A pdb=" N THR O 125 " --> pdb=" O GLU O 10 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AC3, first strand: chain 'C' and resid 83 through 87 removed outlier: 3.660A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AC5, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AC6, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AC7, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.504A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER R 97 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.504A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.578A pdb=" N GLU Q 10 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR Q 125 " --> pdb=" O GLU Q 10 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.578A pdb=" N GLU Q 10 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR Q 125 " --> pdb=" O GLU Q 10 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL Q 117 " --> pdb=" O ARG Q 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.696A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP H 35 " --> pdb=" O ASN H 51 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 127 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.696A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP H 35 " --> pdb=" O ASN H 51 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AD7, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.475A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.475A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1626 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: 2.74 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5058 1.34 - 1.46: 4126 1.46 - 1.58: 7821 1.58 - 1.70: 1 1.70 - 1.82: 172 Bond restraints: 17178 Sorted by residual: bond pdb=" C1 NAG q 1 " pdb=" O5 NAG q 1 " ideal model delta sigma weight residual 1.406 1.338 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1 BMA j 3 " pdb=" C2 BMA j 3 " ideal model delta sigma weight residual 1.519 1.580 -0.061 2.00e-02 2.50e+03 9.37e+00 bond pdb=" C5 BMA q 3 " pdb=" O5 BMA q 3 " ideal model delta sigma weight residual 1.417 1.471 -0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" N LEU a 387 " pdb=" CA LEU a 387 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.27e-02 6.20e+03 7.04e+00 bond pdb=" C1 BMA j 3 " pdb=" O5 BMA j 3 " ideal model delta sigma weight residual 1.410 1.463 -0.053 2.00e-02 2.50e+03 6.91e+00 ... (remaining 17173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 22358 1.95 - 3.91: 711 3.91 - 5.86: 185 5.86 - 7.81: 52 7.81 - 9.76: 5 Bond angle restraints: 23311 Sorted by residual: angle pdb=" C GLN C 223 " pdb=" N ASN C 224 " pdb=" CA ASN C 224 " ideal model delta sigma weight residual 122.67 112.91 9.76 1.73e+00 3.34e-01 3.19e+01 angle pdb=" N ASN C 224 " pdb=" CA ASN C 224 " pdb=" CB ASN C 224 " ideal model delta sigma weight residual 110.46 117.36 -6.90 1.55e+00 4.16e-01 1.98e+01 angle pdb=" CA PHE a 399 " pdb=" CB PHE a 399 " pdb=" CG PHE a 399 " ideal model delta sigma weight residual 113.80 117.96 -4.16 1.00e+00 1.00e+00 1.73e+01 angle pdb=" N ASN C 109 " pdb=" CA ASN C 109 " pdb=" C ASN C 109 " ideal model delta sigma weight residual 113.19 107.16 6.03 1.58e+00 4.01e-01 1.45e+01 angle pdb=" C ASN C 109 " pdb=" CA ASN C 109 " pdb=" CB ASN C 109 " ideal model delta sigma weight residual 110.35 116.71 -6.36 1.78e+00 3.16e-01 1.28e+01 ... (remaining 23306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.30: 10681 25.30 - 50.59: 597 50.59 - 75.89: 131 75.89 - 101.18: 133 101.18 - 126.48: 66 Dihedral angle restraints: 11608 sinusoidal: 5954 harmonic: 5654 Sorted by residual: dihedral pdb=" CB CYS c 364 " pdb=" SG CYS c 364 " pdb=" SG CYS c 385 " pdb=" CB CYS c 385 " ideal model delta sinusoidal sigma weight residual -86.00 -169.06 83.06 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" CB CYS b 364 " pdb=" SG CYS b 364 " pdb=" SG CYS b 385 " pdb=" CB CYS b 385 " ideal model delta sinusoidal sigma weight residual -86.00 -165.52 79.52 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " pdb=" SG CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sinusoidal sigma weight residual -86.00 -164.62 78.62 1 1.00e+01 1.00e-02 7.71e+01 ... (remaining 11605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.244: 2903 0.244 - 0.489: 21 0.489 - 0.733: 0 0.733 - 0.978: 2 0.978 - 1.222: 1 Chirality restraints: 2927 Sorted by residual: chirality pdb=" C1 FUC V 6 " pdb=" O6 NAG V 1 " pdb=" C2 FUC V 6 " pdb=" O5 FUC V 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.39e+02 chirality pdb=" C1 MAN M 5 " pdb=" O2 MAN M 4 " pdb=" C2 MAN M 5 " pdb=" O5 MAN M 5 " both_signs ideal model delta sigma weight residual False 2.40 2.21 0.19 2.00e-02 2.50e+03 8.94e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.41e+01 ... (remaining 2924 not shown) Planarity restraints: 2807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " -0.155 2.00e-02 2.50e+03 1.28e-01 2.04e+02 pdb=" C7 NAG V 1 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " -0.115 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " 0.205 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 2 " 0.139 2.00e-02 2.50e+03 1.15e-01 1.65e+02 pdb=" C7 NAG V 2 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG V 2 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG V 2 " -0.185 2.00e-02 2.50e+03 pdb=" O7 NAG V 2 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 109 " 0.055 2.00e-02 2.50e+03 4.93e-02 3.04e+01 pdb=" CG ASN C 109 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN C 109 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 109 " -0.050 2.00e-02 2.50e+03 pdb=" C1 NAG k 1 " 0.054 2.00e-02 2.50e+03 ... (remaining 2804 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1491 2.74 - 3.28: 16046 3.28 - 3.82: 26818 3.82 - 4.36: 33264 4.36 - 4.90: 57397 Nonbonded interactions: 135016 Sorted by model distance: nonbonded pdb=" OH TYR R 36 " pdb=" OE1 GLN R 89 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASN C 99 " pdb=" N2 NAG n 1 " model vdw 2.253 3.120 nonbonded pdb=" NH2 ARG a 356 " pdb=" O GLY O 108 " model vdw 2.255 3.120 nonbonded pdb=" NH2 ARG b 356 " pdb=" O GLY Q 108 " model vdw 2.258 3.120 nonbonded pdb=" O3 NAG J 2 " pdb=" O2 BMA J 3 " model vdw 2.274 3.040 ... (remaining 135011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'l' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'p' and resid 1) selection = (chain 't' and resid 1) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'K' selection = chain 'N' selection = chain 'W' selection = chain 'd' selection = chain 'e' selection = chain 'h' selection = chain 'm' selection = chain 'n' selection = chain 's' } ncs_group { reference = (chain 'G' and resid 1 through 3) selection = (chain 'X' and resid 1 through 3) selection = (chain 'Z' and resid 1 through 3) selection = (chain 'k' and resid 1 through 3) } ncs_group { reference = (chain 'I' and resid 1 through 5) selection = (chain 'M' and resid 1 through 5) selection = (chain 'V' and resid 1 through 5) selection = (chain 'g' and resid 1 through 5) selection = (chain 'j' and resid 1 through 5) selection = (chain 'q' and resid 1 through 5) selection = (chain 'r' and resid 1 through 5) selection = (chain 'u' and resid 1 through 5) } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 8.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.210 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.006 0.068 17320 Z= 0.304 Angle : 0.948 20.006 23711 Z= 0.410 Chirality : 0.063 1.222 2927 Planarity : 0.005 0.128 2774 Dihedral : 20.946 126.481 7920 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.20), residues: 1916 helix: 1.05 (0.29), residues: 350 sheet: 0.73 (0.24), residues: 506 loop : -0.20 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 282 TYR 0.014 0.001 TYR T 91 PHE 0.021 0.001 PHE a 399 TRP 0.019 0.001 TRP b 386 HIS 0.006 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00647 (17178) covalent geometry : angle 0.86290 (23311) SS BOND : bond 0.00393 ( 26) SS BOND : angle 1.35126 ( 52) hydrogen bonds : bond 0.15152 ( 606) hydrogen bonds : angle 5.85034 ( 1626) link_ALPHA1-2 : bond 0.01110 ( 3) link_ALPHA1-2 : angle 2.62429 ( 9) link_ALPHA1-3 : bond 0.00650 ( 8) link_ALPHA1-3 : angle 1.81617 ( 24) link_ALPHA1-6 : bond 0.00461 ( 9) link_ALPHA1-6 : angle 1.65178 ( 27) link_BETA1-3 : bond 0.01433 ( 1) link_BETA1-3 : angle 2.42952 ( 3) link_BETA1-4 : bond 0.00825 ( 51) link_BETA1-4 : angle 2.62325 ( 153) link_BETA1-6 : bond 0.00598 ( 11) link_BETA1-6 : angle 2.36683 ( 33) link_NAG-ASN : bond 0.01188 ( 33) link_NAG-ASN : angle 4.91483 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 120 GLN cc_start: 0.8364 (pp30) cc_final: 0.7704 (pp30) REVERT: R 24 ARG cc_start: 0.7622 (ttm110) cc_final: 0.7233 (ttm110) REVERT: R 61 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7870 (ttp-110) REVERT: Q 38 ARG cc_start: 0.8464 (ttp-170) cc_final: 0.7508 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 341 average time/residue: 0.7467 time to fit residues: 277.0190 Evaluate side-chains 309 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 307 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain Q residue 73 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN b 295 ASN O 77 ASN c 405 GLN L 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.098466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.074128 restraints weight = 34780.126| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.40 r_work: 0.2828 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17320 Z= 0.181 Angle : 0.786 16.967 23711 Z= 0.350 Chirality : 0.049 0.733 2927 Planarity : 0.004 0.041 2774 Dihedral : 17.492 113.106 4441 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.36 % Allowed : 10.59 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1916 helix: 1.25 (0.29), residues: 350 sheet: 0.82 (0.23), residues: 528 loop : -0.27 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 379 TYR 0.014 0.001 TYR T 91 PHE 0.016 0.001 PHE b 399 TRP 0.010 0.001 TRP b 386 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00410 (17178) covalent geometry : angle 0.71483 (23311) SS BOND : bond 0.00351 ( 26) SS BOND : angle 1.13566 ( 52) hydrogen bonds : bond 0.04063 ( 606) hydrogen bonds : angle 4.68944 ( 1626) link_ALPHA1-2 : bond 0.00105 ( 3) link_ALPHA1-2 : angle 1.84423 ( 9) link_ALPHA1-3 : bond 0.01400 ( 8) link_ALPHA1-3 : angle 1.96538 ( 24) link_ALPHA1-6 : bond 0.00676 ( 9) link_ALPHA1-6 : angle 2.20207 ( 27) link_BETA1-3 : bond 0.01860 ( 1) link_BETA1-3 : angle 1.27048 ( 3) link_BETA1-4 : bond 0.00632 ( 51) link_BETA1-4 : angle 2.42972 ( 153) link_BETA1-6 : bond 0.00598 ( 11) link_BETA1-6 : angle 1.75152 ( 33) link_NAG-ASN : bond 0.00859 ( 33) link_NAG-ASN : angle 3.77873 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 322 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7762 (ttp80) REVERT: S 12 LYS cc_start: 0.8961 (ptpp) cc_final: 0.8743 (ptmm) REVERT: S 90 ASP cc_start: 0.8170 (m-30) cc_final: 0.7886 (m-30) REVERT: S 120 GLN cc_start: 0.8347 (pp30) cc_final: 0.7697 (pp30) REVERT: P 79 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7060 (mm-40) REVERT: P 81 GLU cc_start: 0.8331 (pm20) cc_final: 0.7935 (pp20) REVERT: c 286 ILE cc_start: 0.8704 (pt) cc_final: 0.8422 (pt) REVERT: R 24 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7699 (ttm110) REVERT: R 70 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7624 (mm-30) REVERT: L 41 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7640 (mtp-110) outliers start: 23 outliers final: 3 residues processed: 327 average time/residue: 0.7375 time to fit residues: 262.8305 Evaluate side-chains 314 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 310 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain c residue 402 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 100 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 169 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 295 ASN O 77 ASN C 218 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.072109 restraints weight = 35100.868| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.39 r_work: 0.2843 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17320 Z= 0.163 Angle : 0.748 15.948 23711 Z= 0.330 Chirality : 0.048 0.708 2927 Planarity : 0.004 0.042 2774 Dihedral : 14.367 107.958 4437 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.66 % Allowed : 14.31 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1916 helix: 1.37 (0.29), residues: 353 sheet: 0.68 (0.24), residues: 524 loop : -0.20 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 24 TYR 0.013 0.001 TYR T 91 PHE 0.014 0.001 PHE a 399 TRP 0.009 0.001 TRP Q 109 HIS 0.003 0.001 HIS a 305 Details of bonding type rmsd covalent geometry : bond 0.00368 (17178) covalent geometry : angle 0.68280 (23311) SS BOND : bond 0.00330 ( 26) SS BOND : angle 1.02183 ( 52) hydrogen bonds : bond 0.03643 ( 606) hydrogen bonds : angle 4.40790 ( 1626) link_ALPHA1-2 : bond 0.00228 ( 3) link_ALPHA1-2 : angle 1.87331 ( 9) link_ALPHA1-3 : bond 0.01776 ( 8) link_ALPHA1-3 : angle 1.93993 ( 24) link_ALPHA1-6 : bond 0.00771 ( 9) link_ALPHA1-6 : angle 1.98269 ( 27) link_BETA1-3 : bond 0.01948 ( 1) link_BETA1-3 : angle 1.81256 ( 3) link_BETA1-4 : bond 0.00561 ( 51) link_BETA1-4 : angle 2.27564 ( 153) link_BETA1-6 : bond 0.00569 ( 11) link_BETA1-6 : angle 1.81690 ( 33) link_NAG-ASN : bond 0.00676 ( 33) link_NAG-ASN : angle 3.50202 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 313 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7804 (ttp80) REVERT: T 79 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6850 (mt0) REVERT: T 103 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8409 (ttp80) REVERT: S 12 LYS cc_start: 0.8957 (ptpp) cc_final: 0.8652 (ptmm) REVERT: S 90 ASP cc_start: 0.8155 (m-30) cc_final: 0.7776 (m-30) REVERT: S 120 GLN cc_start: 0.8274 (pp30) cc_final: 0.7737 (pp30) REVERT: P 79 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7181 (mm-40) REVERT: P 81 GLU cc_start: 0.8331 (pm20) cc_final: 0.7977 (pp20) REVERT: C 251 ASP cc_start: 0.8169 (m-30) cc_final: 0.7916 (m-30) REVERT: R 24 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7574 (ttm110) REVERT: R 61 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7340 (ttp-110) REVERT: R 82 ASP cc_start: 0.8158 (m-30) cc_final: 0.7941 (m-30) REVERT: Q 73 ASP cc_start: 0.7536 (t70) cc_final: 0.7121 (t0) REVERT: H 5 ARG cc_start: 0.8075 (mmm160) cc_final: 0.7741 (mmm160) REVERT: H 13 ARG cc_start: 0.8742 (mmm160) cc_final: 0.8264 (mmm160) REVERT: L 41 ARG cc_start: 0.7944 (mtt90) cc_final: 0.7685 (mtp-110) outliers start: 28 outliers final: 9 residues processed: 325 average time/residue: 0.7076 time to fit residues: 251.5263 Evaluate side-chains 316 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 305 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 295 ASN O 77 ASN C 218 GLN R 100 GLN Q 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.098575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.074213 restraints weight = 34998.899| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.42 r_work: 0.2830 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17320 Z= 0.158 Angle : 0.737 15.467 23711 Z= 0.325 Chirality : 0.047 0.701 2927 Planarity : 0.003 0.042 2774 Dihedral : 12.761 104.206 4437 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.71 % Allowed : 16.50 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1916 helix: 1.42 (0.29), residues: 353 sheet: 0.71 (0.24), residues: 522 loop : -0.20 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 24 TYR 0.012 0.001 TYR T 91 PHE 0.013 0.001 PHE b 399 TRP 0.009 0.001 TRP Q 109 HIS 0.003 0.001 HIS a 305 Details of bonding type rmsd covalent geometry : bond 0.00357 (17178) covalent geometry : angle 0.67314 (23311) SS BOND : bond 0.00318 ( 26) SS BOND : angle 1.00397 ( 52) hydrogen bonds : bond 0.03406 ( 606) hydrogen bonds : angle 4.28496 ( 1626) link_ALPHA1-2 : bond 0.00270 ( 3) link_ALPHA1-2 : angle 1.99280 ( 9) link_ALPHA1-3 : bond 0.01832 ( 8) link_ALPHA1-3 : angle 2.01385 ( 24) link_ALPHA1-6 : bond 0.00838 ( 9) link_ALPHA1-6 : angle 1.86461 ( 27) link_BETA1-3 : bond 0.02165 ( 1) link_BETA1-3 : angle 2.06981 ( 3) link_BETA1-4 : bond 0.00567 ( 51) link_BETA1-4 : angle 2.21240 ( 153) link_BETA1-6 : bond 0.00681 ( 11) link_BETA1-6 : angle 1.83114 ( 33) link_NAG-ASN : bond 0.00563 ( 33) link_NAG-ASN : angle 3.43289 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 314 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7797 (ttp80) REVERT: T 103 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8374 (ttp80) REVERT: S 90 ASP cc_start: 0.8168 (m-30) cc_final: 0.7720 (m-30) REVERT: S 120 GLN cc_start: 0.8205 (pp30) cc_final: 0.7628 (pp30) REVERT: B 75 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.7557 (mmt) REVERT: b 331 GLN cc_start: 0.8410 (mp10) cc_final: 0.8027 (pm20) REVERT: P 79 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7168 (mm-40) REVERT: P 81 GLU cc_start: 0.8394 (pm20) cc_final: 0.8037 (pp20) REVERT: C 251 ASP cc_start: 0.8209 (m-30) cc_final: 0.7958 (m-30) REVERT: R 24 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7694 (ttm110) REVERT: R 61 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7307 (ttp-110) REVERT: R 70 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7607 (mm-30) REVERT: Q 73 ASP cc_start: 0.7527 (t70) cc_final: 0.7122 (t0) REVERT: H 5 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7604 (mmm160) REVERT: H 13 ARG cc_start: 0.8726 (mmm160) cc_final: 0.8223 (mmm160) REVERT: L 83 GLU cc_start: 0.7832 (pp20) cc_final: 0.7585 (pp20) outliers start: 29 outliers final: 10 residues processed: 327 average time/residue: 0.7311 time to fit residues: 260.4252 Evaluate side-chains 320 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 308 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain H residue 111 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 80 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 295 ASN O 77 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.063220 restraints weight = 33116.764| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.38 r_work: 0.2763 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 17320 Z= 0.283 Angle : 0.822 18.382 23711 Z= 0.368 Chirality : 0.051 0.817 2927 Planarity : 0.004 0.047 2774 Dihedral : 12.209 106.275 4437 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.96 % Allowed : 16.91 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.20), residues: 1916 helix: 1.25 (0.29), residues: 350 sheet: 0.70 (0.23), residues: 518 loop : -0.30 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 24 TYR 0.019 0.002 TYR T 91 PHE 0.018 0.002 PHE a 399 TRP 0.012 0.001 TRP H 35 HIS 0.004 0.001 HIS a 305 Details of bonding type rmsd covalent geometry : bond 0.00666 (17178) covalent geometry : angle 0.75548 (23311) SS BOND : bond 0.00445 ( 26) SS BOND : angle 1.52695 ( 52) hydrogen bonds : bond 0.04181 ( 606) hydrogen bonds : angle 4.44558 ( 1626) link_ALPHA1-2 : bond 0.00168 ( 3) link_ALPHA1-2 : angle 2.08306 ( 9) link_ALPHA1-3 : bond 0.01852 ( 8) link_ALPHA1-3 : angle 2.03906 ( 24) link_ALPHA1-6 : bond 0.00832 ( 9) link_ALPHA1-6 : angle 1.90495 ( 27) link_BETA1-3 : bond 0.02504 ( 1) link_BETA1-3 : angle 2.28033 ( 3) link_BETA1-4 : bond 0.00549 ( 51) link_BETA1-4 : angle 2.30742 ( 153) link_BETA1-6 : bond 0.00623 ( 11) link_BETA1-6 : angle 2.01165 ( 33) link_NAG-ASN : bond 0.00829 ( 33) link_NAG-ASN : angle 3.75959 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 313 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: a 282 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.8230 (ttp-110) REVERT: T 24 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7826 (ttp80) REVERT: T 103 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8342 (ttp80) REVERT: S 3 GLN cc_start: 0.9048 (pm20) cc_final: 0.8812 (pm20) REVERT: S 90 ASP cc_start: 0.8286 (m-30) cc_final: 0.7810 (m-30) REVERT: b 331 GLN cc_start: 0.8441 (mp10) cc_final: 0.8055 (pm20) REVERT: P 81 GLU cc_start: 0.8413 (pm20) cc_final: 0.8151 (pm20) REVERT: O 3 GLN cc_start: 0.8841 (pm20) cc_final: 0.8468 (pm20) REVERT: O 38 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8106 (ttm170) REVERT: R 24 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7660 (ttm110) REVERT: Q 73 ASP cc_start: 0.7760 (t70) cc_final: 0.7397 (t0) REVERT: Q 90 ASP cc_start: 0.8184 (m-30) cc_final: 0.7983 (m-30) REVERT: H 5 ARG cc_start: 0.7987 (mmm160) cc_final: 0.7727 (mmm160) REVERT: H 13 ARG cc_start: 0.8717 (mmm160) cc_final: 0.8248 (mmm160) outliers start: 50 outliers final: 20 residues processed: 337 average time/residue: 0.7076 time to fit residues: 260.7687 Evaluate side-chains 327 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 305 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 379 ARG Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 39 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 184 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 295 ASN O 77 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.065772 restraints weight = 32752.366| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.37 r_work: 0.2815 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17320 Z= 0.148 Angle : 0.738 15.975 23711 Z= 0.329 Chirality : 0.047 0.726 2927 Planarity : 0.003 0.043 2774 Dihedral : 11.305 101.391 4437 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.37 % Allowed : 18.39 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.20), residues: 1916 helix: 1.41 (0.29), residues: 353 sheet: 0.73 (0.23), residues: 518 loop : -0.28 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG P 24 TYR 0.024 0.001 TYR P 49 PHE 0.012 0.001 PHE b 399 TRP 0.012 0.001 TRP C 210 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00327 (17178) covalent geometry : angle 0.67589 (23311) SS BOND : bond 0.00291 ( 26) SS BOND : angle 0.95683 ( 52) hydrogen bonds : bond 0.03304 ( 606) hydrogen bonds : angle 4.26989 ( 1626) link_ALPHA1-2 : bond 0.00337 ( 3) link_ALPHA1-2 : angle 2.12289 ( 9) link_ALPHA1-3 : bond 0.01992 ( 8) link_ALPHA1-3 : angle 2.14800 ( 24) link_ALPHA1-6 : bond 0.00971 ( 9) link_ALPHA1-6 : angle 1.83249 ( 27) link_BETA1-3 : bond 0.03045 ( 1) link_BETA1-3 : angle 3.46940 ( 3) link_BETA1-4 : bond 0.00584 ( 51) link_BETA1-4 : angle 2.10247 ( 153) link_BETA1-6 : bond 0.00662 ( 11) link_BETA1-6 : angle 1.70008 ( 33) link_NAG-ASN : bond 0.00783 ( 33) link_NAG-ASN : angle 3.42163 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 316 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7838 (ttp80) REVERT: T 103 ARG cc_start: 0.8577 (ttp80) cc_final: 0.8320 (ttp80) REVERT: S 3 GLN cc_start: 0.9042 (pm20) cc_final: 0.8834 (pm20) REVERT: S 90 ASP cc_start: 0.8286 (m-30) cc_final: 0.7847 (m-30) REVERT: b 331 GLN cc_start: 0.8435 (mp10) cc_final: 0.8058 (pm20) REVERT: P 81 GLU cc_start: 0.8452 (pm20) cc_final: 0.8115 (pp20) REVERT: O 90 ASP cc_start: 0.7715 (m-30) cc_final: 0.7327 (m-30) REVERT: C 251 ASP cc_start: 0.8181 (m-30) cc_final: 0.7956 (m-30) REVERT: R 24 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7592 (ttm110) REVERT: Q 73 ASP cc_start: 0.7692 (t70) cc_final: 0.7333 (t0) REVERT: Q 90 ASP cc_start: 0.8181 (m-30) cc_final: 0.7957 (m-30) REVERT: H 5 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7698 (mmm160) REVERT: H 13 ARG cc_start: 0.8693 (mmm160) cc_final: 0.8223 (mmm160) REVERT: L 56 ARG cc_start: 0.8925 (mtm-85) cc_final: 0.8508 (mtm110) outliers start: 40 outliers final: 13 residues processed: 338 average time/residue: 0.7082 time to fit residues: 263.5642 Evaluate side-chains 322 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 308 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 23 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 295 ASN O 77 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.092863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.065857 restraints weight = 32893.983| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.39 r_work: 0.2792 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17320 Z= 0.143 Angle : 0.729 15.202 23711 Z= 0.327 Chirality : 0.047 0.698 2927 Planarity : 0.004 0.054 2774 Dihedral : 10.539 100.424 4437 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.48 % Allowed : 18.75 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1916 helix: 1.47 (0.29), residues: 353 sheet: 0.80 (0.24), residues: 515 loop : -0.24 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG a 282 TYR 0.027 0.001 TYR P 49 PHE 0.012 0.001 PHE b 399 TRP 0.015 0.001 TRP C 210 HIS 0.003 0.001 HIS a 305 Details of bonding type rmsd covalent geometry : bond 0.00317 (17178) covalent geometry : angle 0.67022 (23311) SS BOND : bond 0.00284 ( 26) SS BOND : angle 0.89853 ( 52) hydrogen bonds : bond 0.03195 ( 606) hydrogen bonds : angle 4.17118 ( 1626) link_ALPHA1-2 : bond 0.00364 ( 3) link_ALPHA1-2 : angle 2.18453 ( 9) link_ALPHA1-3 : bond 0.02003 ( 8) link_ALPHA1-3 : angle 2.21737 ( 24) link_ALPHA1-6 : bond 0.01056 ( 9) link_ALPHA1-6 : angle 1.73457 ( 27) link_BETA1-3 : bond 0.03110 ( 1) link_BETA1-3 : angle 3.68092 ( 3) link_BETA1-4 : bond 0.00623 ( 51) link_BETA1-4 : angle 2.12206 ( 153) link_BETA1-6 : bond 0.00617 ( 11) link_BETA1-6 : angle 1.62064 ( 33) link_NAG-ASN : bond 0.00716 ( 33) link_NAG-ASN : angle 3.23729 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 315 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7844 (ttp80) REVERT: T 30 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8021 (pp) REVERT: T 103 ARG cc_start: 0.8600 (ttp80) cc_final: 0.8348 (ttp80) REVERT: S 90 ASP cc_start: 0.8372 (m-30) cc_final: 0.7955 (m-30) REVERT: b 331 GLN cc_start: 0.8438 (mp10) cc_final: 0.8003 (pm20) REVERT: P 79 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7288 (mm110) REVERT: P 81 GLU cc_start: 0.8452 (pm20) cc_final: 0.8151 (pp20) REVERT: C 251 ASP cc_start: 0.8164 (m-30) cc_final: 0.7949 (m-30) REVERT: c 405 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8332 (tp-100) REVERT: R 24 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7619 (ttm110) REVERT: Q 73 ASP cc_start: 0.7752 (t70) cc_final: 0.7385 (OUTLIER) REVERT: Q 90 ASP cc_start: 0.8232 (m-30) cc_final: 0.7981 (m-30) REVERT: H 5 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7687 (mmm160) REVERT: H 13 ARG cc_start: 0.8677 (mmm160) cc_final: 0.8219 (mmm160) REVERT: L 56 ARG cc_start: 0.8918 (mtm-85) cc_final: 0.8552 (mtm110) outliers start: 42 outliers final: 20 residues processed: 344 average time/residue: 0.6910 time to fit residues: 260.4469 Evaluate side-chains 328 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 307 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 175 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 295 ASN O 77 ASN C 218 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.090230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.062835 restraints weight = 33358.944| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.42 r_work: 0.2728 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 17320 Z= 0.278 Angle : 0.825 18.384 23711 Z= 0.374 Chirality : 0.051 0.823 2927 Planarity : 0.004 0.055 2774 Dihedral : 10.581 101.353 4437 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.48 % Allowed : 19.22 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 1916 helix: 1.27 (0.29), residues: 350 sheet: 0.66 (0.23), residues: 518 loop : -0.32 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG a 282 TYR 0.026 0.002 TYR P 49 PHE 0.018 0.002 PHE a 399 TRP 0.017 0.001 TRP C 210 HIS 0.004 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00650 (17178) covalent geometry : angle 0.76288 (23311) SS BOND : bond 0.00425 ( 26) SS BOND : angle 1.48782 ( 52) hydrogen bonds : bond 0.04110 ( 606) hydrogen bonds : angle 4.38669 ( 1626) link_ALPHA1-2 : bond 0.00212 ( 3) link_ALPHA1-2 : angle 2.27654 ( 9) link_ALPHA1-3 : bond 0.01854 ( 8) link_ALPHA1-3 : angle 2.12295 ( 24) link_ALPHA1-6 : bond 0.00959 ( 9) link_ALPHA1-6 : angle 1.64315 ( 27) link_BETA1-3 : bond 0.03005 ( 1) link_BETA1-3 : angle 3.30663 ( 3) link_BETA1-4 : bond 0.00562 ( 51) link_BETA1-4 : angle 2.22887 ( 153) link_BETA1-6 : bond 0.00535 ( 11) link_BETA1-6 : angle 1.88840 ( 33) link_NAG-ASN : bond 0.00993 ( 33) link_NAG-ASN : angle 3.64408 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 305 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 282 ARG cc_start: 0.8619 (ttp-110) cc_final: 0.8236 (ttp-110) REVERT: T 24 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7883 (ttp80) REVERT: T 30 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8014 (pp) REVERT: T 103 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8389 (ttp80) REVERT: S 90 ASP cc_start: 0.8466 (m-30) cc_final: 0.8066 (m-30) REVERT: b 331 GLN cc_start: 0.8471 (mp10) cc_final: 0.8075 (pm20) REVERT: P 81 GLU cc_start: 0.8449 (pm20) cc_final: 0.8178 (pm20) REVERT: O 38 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8231 (ttm170) REVERT: c 295 ASN cc_start: 0.8800 (p0) cc_final: 0.8569 (p0) REVERT: c 414 MET cc_start: 0.8715 (tmm) cc_final: 0.8344 (ttp) REVERT: R 24 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7672 (ttm110) REVERT: Q 73 ASP cc_start: 0.7819 (t70) cc_final: 0.7458 (OUTLIER) REVERT: Q 90 ASP cc_start: 0.8259 (m-30) cc_final: 0.7975 (m-30) REVERT: H 5 ARG cc_start: 0.8036 (mmm160) cc_final: 0.7741 (mmm160) REVERT: H 13 ARG cc_start: 0.8682 (mmm160) cc_final: 0.8209 (mmm160) outliers start: 42 outliers final: 19 residues processed: 333 average time/residue: 0.7112 time to fit residues: 258.9316 Evaluate side-chains 320 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 299 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain Q residue 62 GLN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 170 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 77 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.091762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.064418 restraints weight = 33113.056| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.42 r_work: 0.2760 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17320 Z= 0.177 Angle : 0.762 16.735 23711 Z= 0.346 Chirality : 0.048 0.764 2927 Planarity : 0.004 0.053 2774 Dihedral : 10.125 100.821 4437 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.19 % Allowed : 20.28 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 1916 helix: 1.32 (0.29), residues: 353 sheet: 0.67 (0.23), residues: 518 loop : -0.32 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 24 TYR 0.026 0.001 TYR P 49 PHE 0.012 0.001 PHE a 399 TRP 0.021 0.001 TRP C 210 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00402 (17178) covalent geometry : angle 0.70380 (23311) SS BOND : bond 0.00323 ( 26) SS BOND : angle 1.06877 ( 52) hydrogen bonds : bond 0.03509 ( 606) hydrogen bonds : angle 4.28388 ( 1626) link_ALPHA1-2 : bond 0.00336 ( 3) link_ALPHA1-2 : angle 2.26615 ( 9) link_ALPHA1-3 : bond 0.01983 ( 8) link_ALPHA1-3 : angle 2.22031 ( 24) link_ALPHA1-6 : bond 0.00984 ( 9) link_ALPHA1-6 : angle 1.60143 ( 27) link_BETA1-3 : bond 0.03212 ( 1) link_BETA1-3 : angle 3.58093 ( 3) link_BETA1-4 : bond 0.00579 ( 51) link_BETA1-4 : angle 2.08260 ( 153) link_BETA1-6 : bond 0.00620 ( 11) link_BETA1-6 : angle 1.55867 ( 33) link_NAG-ASN : bond 0.00905 ( 33) link_NAG-ASN : angle 3.40988 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 311 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 282 ARG cc_start: 0.8594 (ttp-110) cc_final: 0.8188 (ttp-110) REVERT: T 24 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7889 (ttp80) REVERT: T 30 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7972 (pp) REVERT: T 103 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8359 (ttp80) REVERT: S 90 ASP cc_start: 0.8472 (m-30) cc_final: 0.8073 (m-30) REVERT: b 331 GLN cc_start: 0.8467 (mp10) cc_final: 0.8106 (pm20) REVERT: P 81 GLU cc_start: 0.8472 (pm20) cc_final: 0.8225 (pm20) REVERT: C 209 ASN cc_start: 0.7417 (m110) cc_final: 0.7149 (m-40) REVERT: C 251 ASP cc_start: 0.8176 (m-30) cc_final: 0.7968 (m-30) REVERT: c 295 ASN cc_start: 0.8819 (p0) cc_final: 0.8591 (p0) REVERT: R 24 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7654 (ttm110) REVERT: R 61 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7574 (ttp-110) REVERT: Q 73 ASP cc_start: 0.7773 (t70) cc_final: 0.7410 (OUTLIER) REVERT: Q 90 ASP cc_start: 0.8262 (m-30) cc_final: 0.7967 (m-30) REVERT: H 5 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7704 (mmm160) REVERT: H 13 ARG cc_start: 0.8666 (mmm160) cc_final: 0.8221 (mmm160) REVERT: L 49 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7018 (mtt) REVERT: L 56 ARG cc_start: 0.8933 (mtm-85) cc_final: 0.8516 (mtm110) outliers start: 37 outliers final: 22 residues processed: 332 average time/residue: 0.7125 time to fit residues: 258.7206 Evaluate side-chains 331 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 307 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 106 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 30 optimal weight: 0.0870 chunk 156 optimal weight: 9.9990 chunk 52 optimal weight: 0.2980 chunk 153 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 77 ASN R 100 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.093926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.066710 restraints weight = 32757.651| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.42 r_work: 0.2808 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17320 Z= 0.130 Angle : 0.720 14.618 23711 Z= 0.327 Chirality : 0.046 0.669 2927 Planarity : 0.004 0.054 2774 Dihedral : 9.487 98.669 4437 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.71 % Allowed : 21.17 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1916 helix: 1.48 (0.29), residues: 353 sheet: 0.73 (0.24), residues: 518 loop : -0.27 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG a 379 TYR 0.028 0.001 TYR P 49 PHE 0.010 0.001 PHE b 399 TRP 0.022 0.001 TRP C 210 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00281 (17178) covalent geometry : angle 0.66591 (23311) SS BOND : bond 0.00261 ( 26) SS BOND : angle 0.77343 ( 52) hydrogen bonds : bond 0.02987 ( 606) hydrogen bonds : angle 4.12172 ( 1626) link_ALPHA1-2 : bond 0.00533 ( 3) link_ALPHA1-2 : angle 2.26184 ( 9) link_ALPHA1-3 : bond 0.02053 ( 8) link_ALPHA1-3 : angle 2.31992 ( 24) link_ALPHA1-6 : bond 0.01051 ( 9) link_ALPHA1-6 : angle 1.61056 ( 27) link_BETA1-3 : bond 0.03162 ( 1) link_BETA1-3 : angle 3.69997 ( 3) link_BETA1-4 : bond 0.00623 ( 51) link_BETA1-4 : angle 1.99225 ( 153) link_BETA1-6 : bond 0.00585 ( 11) link_BETA1-6 : angle 1.37742 ( 33) link_NAG-ASN : bond 0.00782 ( 33) link_NAG-ASN : angle 3.15224 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 316 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7921 (ttp80) REVERT: T 103 ARG cc_start: 0.8569 (ttp80) cc_final: 0.8096 (ttp80) REVERT: T 105 ASP cc_start: 0.8052 (t0) cc_final: 0.7696 (p0) REVERT: S 90 ASP cc_start: 0.8435 (m-30) cc_final: 0.8056 (m-30) REVERT: B 122 ASP cc_start: 0.8754 (t0) cc_final: 0.8447 (t0) REVERT: B 126 LYS cc_start: 0.8797 (mttp) cc_final: 0.8503 (mttp) REVERT: b 331 GLN cc_start: 0.8436 (mp10) cc_final: 0.8005 (pm20) REVERT: P 81 GLU cc_start: 0.8509 (pm20) cc_final: 0.8263 (pm20) REVERT: C 251 ASP cc_start: 0.8177 (m-30) cc_final: 0.7956 (m-30) REVERT: c 295 ASN cc_start: 0.8802 (p0) cc_final: 0.8552 (p0) REVERT: c 414 MET cc_start: 0.8648 (tmm) cc_final: 0.8292 (ttp) REVERT: R 24 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7631 (ttm110) REVERT: R 61 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7703 (ttp-110) REVERT: Q 73 ASP cc_start: 0.7735 (t70) cc_final: 0.7378 (OUTLIER) REVERT: Q 90 ASP cc_start: 0.8188 (m-30) cc_final: 0.7902 (m-30) REVERT: H 5 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7687 (mmm160) REVERT: H 13 ARG cc_start: 0.8654 (mmm160) cc_final: 0.8221 (mmm160) REVERT: H 119 ASP cc_start: 0.8212 (t0) cc_final: 0.7936 (t70) REVERT: L 49 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6938 (mtt) REVERT: L 56 ARG cc_start: 0.8894 (mtm-85) cc_final: 0.8530 (mtm110) outliers start: 29 outliers final: 18 residues processed: 336 average time/residue: 0.6944 time to fit residues: 255.3208 Evaluate side-chains 328 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 309 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 77 ASN C 218 GLN C 247 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.092847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065779 restraints weight = 32962.621| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.39 r_work: 0.2791 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17320 Z= 0.168 Angle : 0.748 15.095 23711 Z= 0.339 Chirality : 0.047 0.701 2927 Planarity : 0.004 0.059 2774 Dihedral : 9.444 98.491 4437 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.42 % Allowed : 21.53 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1916 helix: 1.49 (0.29), residues: 353 sheet: 0.74 (0.23), residues: 518 loop : -0.27 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG a 282 TYR 0.028 0.001 TYR P 49 PHE 0.012 0.001 PHE b 399 TRP 0.024 0.001 TRP C 210 HIS 0.003 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00383 (17178) covalent geometry : angle 0.69478 (23311) SS BOND : bond 0.00299 ( 26) SS BOND : angle 0.93598 ( 52) hydrogen bonds : bond 0.03233 ( 606) hydrogen bonds : angle 4.12737 ( 1626) link_ALPHA1-2 : bond 0.00475 ( 3) link_ALPHA1-2 : angle 2.33027 ( 9) link_ALPHA1-3 : bond 0.02012 ( 8) link_ALPHA1-3 : angle 2.26512 ( 24) link_ALPHA1-6 : bond 0.01026 ( 9) link_ALPHA1-6 : angle 1.60117 ( 27) link_BETA1-3 : bond 0.03132 ( 1) link_BETA1-3 : angle 3.66465 ( 3) link_BETA1-4 : bond 0.00582 ( 51) link_BETA1-4 : angle 2.00318 ( 153) link_BETA1-6 : bond 0.00507 ( 11) link_BETA1-6 : angle 1.43700 ( 33) link_NAG-ASN : bond 0.00821 ( 33) link_NAG-ASN : angle 3.21199 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6222.25 seconds wall clock time: 106 minutes 39.88 seconds (6399.88 seconds total)