Starting phenix.real_space_refine on Sat Jul 4 10:46:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8euv_28618/07_2026/8euv_28618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euv_28618/07_2026/8euv_28618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8euv_28618/07_2026/8euv_28618.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8euv_28618/07_2026/8euv_28618.cif" model { file = "/net/cci-nas-00/data/ceres_data/8euv_28618/07_2026/8euv_28618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euv_28618/07_2026/8euv_28618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8euv_28618/07_2026/8euv_28618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euv_28618/07_2026/8euv_28618.map" } resolution = 2.6 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 12486 2.51 5 N 3342 2.21 5 O 4181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20138 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "G" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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 chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 4.53, per 1000 atoms: 0.22 Number of scatterers: 20138 At special positions: 0 Unit cell: (153.55, 142.76, 121.18, 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 129 16.00 O 4181 8.00 N 3342 7.00 C 12486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=1.85 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.05 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA m 3 " - " MAN m 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 276 " " NAG Z 1 " - " ASN C 386 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 295 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 332 " " NAG f 1 " - " ASN C 363 " " NAG g 1 " - " ASN E 295 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 386 " " NAG m 1 " - " ASN E 262 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 332 " " NAG p 1 " - " ASN E 363 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 990.3 milliseconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 45 sheets defined 17.9% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.940A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.941A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.505A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.640A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 639 through 662 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.929A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.065A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.508A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.619A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 639 through 662 Processing helix chain 'E' and resid 98 through 116 removed outlier: 3.940A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.011A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.504A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.978A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.719A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 595 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 639 through 662 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.997A pdb=" N ASN G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.992A pdb=" N ASN I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.990A pdb=" N ASN K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.344A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.602A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.788A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.419A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.377A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.930A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.956A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.191A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.956A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.930A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.521A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.501A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.589A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.810A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.418A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.378A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.947A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.781A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 12.195A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 12.195A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.781A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.947A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.522A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.209A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.590A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.790A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.416A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.378A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.075A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 12.193A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 273 removed outlier: 12.193A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 11.075A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.957A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.522A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.512A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.767A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 removed outlier: 12.015A pdb=" N CYS H 23 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 10.985A pdb=" N THR H 74 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 12.093A pdb=" N ALA H 25 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N THR H 72 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N GLN H 27 " --> pdb=" O HIS H 70 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N HIS H 70 " --> pdb=" O GLN H 27 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.706A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.758A pdb=" N THR H 97 " --> pdb=" O HIS H 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.525A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.749A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 removed outlier: 12.005A pdb=" N CYS J 23 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N THR J 74 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 12.105A pdb=" N ALA J 25 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR J 72 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N GLN J 27 " --> pdb=" O HIS J 70 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N HIS J 70 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.717A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.766A pdb=" N THR J 97 " --> pdb=" O HIS J 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.511A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.759A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 4 through 7 removed outlier: 12.055A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 12.142A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.762A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N GLN L 27 " --> pdb=" O HIS L 70 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N HIS L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.724A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.768A pdb=" N THR L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2070 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: 4.21 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.61: 20158 1.61 - 1.99: 176 1.99 - 2.37: 1 2.37 - 2.75: 0 2.75 - 3.14: 2 Bond restraints: 20337 Sorted by residual: bond pdb=" N PRO H 8 " pdb=" CD PRO H 8 " ideal model delta sigma weight residual 1.474 3.137 -1.663 1.40e-02 5.10e+03 1.41e+04 bond pdb=" N PRO J 8 " pdb=" CD PRO J 8 " ideal model delta sigma weight residual 1.474 2.946 -1.472 1.40e-02 5.10e+03 1.11e+04 bond pdb=" CB PRO H 8 " pdb=" CG PRO H 8 " ideal model delta sigma weight residual 1.506 2.053 -0.547 3.90e-02 6.57e+02 1.96e+02 bond pdb=" CB PRO J 8 " pdb=" CG PRO J 8 " ideal model delta sigma weight residual 1.506 1.933 -0.427 3.90e-02 6.57e+02 1.20e+02 bond pdb=" N PRO H 59 " pdb=" CD PRO H 59 " ideal model delta sigma weight residual 1.473 1.622 -0.149 1.40e-02 5.10e+03 1.13e+02 ... (remaining 20332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.55: 27594 16.55 - 33.11: 7 33.11 - 49.66: 0 49.66 - 66.21: 0 66.21 - 82.77: 2 Bond angle restraints: 27603 Sorted by residual: angle pdb=" N PRO H 8 " pdb=" CD PRO H 8 " pdb=" CG PRO H 8 " ideal model delta sigma weight residual 103.80 21.03 82.77 1.20e+00 6.94e-01 4.76e+03 angle pdb=" N PRO J 8 " pdb=" CD PRO J 8 " pdb=" CG PRO J 8 " ideal model delta sigma weight residual 103.80 36.76 67.04 1.20e+00 6.94e-01 3.12e+03 angle pdb=" CA PRO H 8 " pdb=" N PRO H 8 " pdb=" CD PRO H 8 " ideal model delta sigma weight residual 111.50 86.14 25.36 1.40e+00 5.10e-01 3.28e+02 angle pdb=" CA PRO J 8 " pdb=" N PRO J 8 " pdb=" CD PRO J 8 " ideal model delta sigma weight residual 111.50 88.42 23.08 1.40e+00 5.10e-01 2.72e+02 angle pdb=" CB PRO H 8 " pdb=" CG PRO H 8 " pdb=" CD PRO H 8 " ideal model delta sigma weight residual 105.40 78.06 27.34 2.30e+00 1.89e-01 1.41e+02 ... (remaining 27598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.29: 10847 27.29 - 54.58: 569 54.58 - 81.87: 53 81.87 - 109.17: 4 109.17 - 136.46: 2 Dihedral angle restraints: 11475 sinusoidal: 4590 harmonic: 6885 Sorted by residual: dihedral pdb=" CA ASN D 618 " pdb=" C ASN D 618 " pdb=" N LEU D 619 " pdb=" CA LEU D 619 " ideal model delta harmonic sigma weight residual -180.00 -135.65 -44.35 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -6.74 -79.26 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CA ASN B 618 " pdb=" C ASN B 618 " pdb=" N LEU B 619 " pdb=" CA LEU B 619 " ideal model delta harmonic sigma weight residual -180.00 -136.28 -43.72 0 5.00e+00 4.00e-02 7.64e+01 ... (remaining 11472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2729 0.060 - 0.120: 501 0.120 - 0.180: 110 0.180 - 0.240: 3 0.240 - 0.299: 8 Chirality restraints: 3351 Sorted by residual: chirality pdb=" C1 MAN R 4 " pdb=" O3 BMA R 3 " pdb=" C2 MAN R 4 " pdb=" O5 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.40 2.43 -0.03 2.00e-02 2.50e+03 2.76e+00 chirality pdb=" C5 BMA m 3 " pdb=" C4 BMA m 3 " pdb=" C6 BMA m 3 " pdb=" O5 BMA m 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 3348 not shown) Planarity restraints: 3447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 13 " -0.085 5.00e-02 4.00e+02 1.28e-01 2.60e+01 pdb=" N PRO K 14 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO K 14 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO K 14 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 7 " -0.060 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO H 8 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO H 8 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 8 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 75 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO E 76 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 76 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 76 " -0.029 5.00e-02 4.00e+02 ... (remaining 3444 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 425 2.68 - 3.24: 17949 3.24 - 3.79: 31436 3.79 - 4.35: 46106 4.35 - 4.90: 73105 Nonbonded interactions: 169021 Sorted by model distance: nonbonded pdb=" OG SER C 56 " pdb=" OG1 THR C 71 " model vdw 2.127 3.040 nonbonded pdb=" OG SER A 56 " pdb=" OG1 THR A 71 " model vdw 2.130 3.040 nonbonded pdb=" OG SER E 56 " pdb=" OG1 THR E 71 " model vdw 2.131 3.040 nonbonded pdb=" O GLN E 293 " pdb=" O HOH E 701 " model vdw 2.168 3.040 nonbonded pdb=" O GLN A 293 " pdb=" O HOH A 701 " model vdw 2.181 3.040 ... (remaining 169016 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'j' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.470 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 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:8.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.017 1.663 20466 Z= 1.152 Angle : 1.145 82.766 27948 Z= 0.705 Chirality : 0.053 0.299 3351 Planarity : 0.005 0.128 3402 Dihedral : 15.342 136.457 6915 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.62 % Allowed : 10.17 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.16 (0.17), residues: 2352 helix: 0.50 (0.27), residues: 408 sheet: 0.59 (0.18), residues: 765 loop : -0.28 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 30 TYR 0.010 0.002 TYR F 638 PHE 0.024 0.002 PHE A 53 TRP 0.013 0.001 TRP E 69 HIS 0.006 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.01742 / 1.15 (20337) covalent geometry : angle 1.10763 / 0.70 (27603) SS BOND : bond 0.02911 / 0.98 ( 42) SS BOND : angle 2.38360 / 1.81 ( 84) hydrogen bonds : bond 0.10861 / 7.29 ( 723) hydrogen bonds : angle 5.95066 / 4.14 ( 2070) link_ALPHA1-2 : bond 0.00202 / 0.08 ( 3) link_ALPHA1-2 : angle 2.01553 / 1.16 ( 9) link_ALPHA1-3 : bond 0.00233 / 0.11 ( 3) link_ALPHA1-3 : angle 2.09442 / 1.19 ( 9) link_BETA1-4 : bond 0.00343 / 0.21 ( 36) link_BETA1-4 : angle 2.10428 / 1.42 ( 108) link_NAG-ASN : bond 0.00373 / 0.22 ( 45) link_NAG-ASN : angle 3.62570 / 2.48 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 254 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8579 (mtp-110) cc_final: 0.7439 (mtm110) REVERT: G 75 ILE cc_start: 0.8202 (pt) cc_final: 0.7959 (pp) REVERT: I 75 ILE cc_start: 0.8316 (pt) cc_final: 0.7933 (pp) outliers start: 13 outliers final: 11 residues processed: 267 average time/residue: 0.5731 time to fit residues: 174.8836 Evaluate side-chains 246 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 235 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain K residue 11 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN D 611 ASN E 67 ASN E 137 ASN E 422 GLN F 591 GLN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.176752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121121 restraints weight = 21436.372| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.17 r_work: 0.3331 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20466 Z= 0.158 Angle : 0.657 12.058 27948 Z= 0.325 Chirality : 0.045 0.285 3351 Planarity : 0.004 0.080 3402 Dihedral : 5.288 35.805 2567 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.45 % Allowed : 9.83 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.70 (0.18), residues: 2352 helix: 1.05 (0.27), residues: 405 sheet: 0.79 (0.18), residues: 795 loop : 0.12 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.011 0.001 TYR C 318 PHE 0.015 0.002 PHE E 53 TRP 0.018 0.001 TRP A 427 HIS 0.004 0.001 HIS H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (20337) covalent geometry : angle 0.61265 / 0.32 (27603) SS BOND : bond 0.00481 / 0.36 ( 42) SS BOND : angle 0.86558 / 0.56 ( 84) hydrogen bonds : bond 0.04331 / 2.96 ( 723) hydrogen bonds : angle 4.99815 / 3.47 ( 2070) link_ALPHA1-2 : bond 0.00484 / 0.23 ( 3) link_ALPHA1-2 : angle 1.83845 / 1.05 ( 9) link_ALPHA1-3 : bond 0.00298 / 0.14 ( 3) link_ALPHA1-3 : angle 1.54110 / 0.96 ( 9) link_BETA1-4 : bond 0.00459 / 0.30 ( 36) link_BETA1-4 : angle 1.54790 / 1.04 ( 108) link_NAG-ASN : bond 0.00351 / 0.22 ( 45) link_NAG-ASN : angle 3.12867 / 2.15 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 262 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8497 (mtp) cc_final: 0.8272 (mtp) REVERT: B 542 ARG cc_start: 0.8511 (mtp-110) cc_final: 0.7190 (mtm110) REVERT: B 632 ASP cc_start: 0.8356 (t70) cc_final: 0.8133 (t0) REVERT: B 658 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6635 (tm-30) REVERT: C 103 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: D 542 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7730 (mtt90) REVERT: E 103 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: E 327 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7851 (ptt-90) REVERT: G 75 ILE cc_start: 0.8009 (pt) cc_final: 0.7763 (pp) REVERT: L 79 GLN cc_start: 0.5343 (OUTLIER) cc_final: 0.4907 (tp40) outliers start: 51 outliers final: 20 residues processed: 293 average time/residue: 0.6138 time to fit residues: 204.2842 Evaluate side-chains 272 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 198 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 137 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN D 611 ASN E 136 ASN E 137 ASN G 76 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN K 76 ASN L 45 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.176809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124230 restraints weight = 21439.466| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.19 r_work: 0.3304 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20466 Z= 0.145 Angle : 0.607 8.359 27948 Z= 0.299 Chirality : 0.044 0.262 3351 Planarity : 0.004 0.062 3402 Dihedral : 4.962 36.265 2558 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.83 % Allowed : 11.41 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.84 (0.18), residues: 2352 helix: 1.24 (0.27), residues: 405 sheet: 0.85 (0.18), residues: 795 loop : 0.22 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.012 0.001 TYR C 318 PHE 0.014 0.002 PHE E 53 TRP 0.016 0.001 TRP C 427 HIS 0.003 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (20337) covalent geometry : angle 0.56271 / 0.29 (27603) SS BOND : bond 0.00284 / 0.18 ( 42) SS BOND : angle 1.11417 / 0.77 ( 84) hydrogen bonds : bond 0.04040 / 2.76 ( 723) hydrogen bonds : angle 4.79157 / 3.32 ( 2070) link_ALPHA1-2 : bond 0.00317 / 0.14 ( 3) link_ALPHA1-2 : angle 1.43400 / 0.84 ( 9) link_ALPHA1-3 : bond 0.00344 / 0.15 ( 3) link_ALPHA1-3 : angle 1.36554 / 0.83 ( 9) link_BETA1-4 : bond 0.00440 / 0.29 ( 36) link_BETA1-4 : angle 1.45290 / 0.99 ( 108) link_NAG-ASN : bond 0.00324 / 0.21 ( 45) link_NAG-ASN : angle 2.96674 / 2.04 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 255 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: A 178 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7902 (tpt170) REVERT: A 327 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7849 (ptt-90) REVERT: B 542 ARG cc_start: 0.8471 (mtp-110) cc_final: 0.7131 (mtt90) REVERT: B 632 ASP cc_start: 0.8481 (t70) cc_final: 0.8207 (t0) REVERT: B 655 LYS cc_start: 0.6799 (mtmt) cc_final: 0.5215 (pttt) REVERT: C 66 HIS cc_start: 0.6125 (OUTLIER) cc_final: 0.5871 (m90) REVERT: C 103 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: E 95 MET cc_start: 0.8964 (ptm) cc_final: 0.8658 (ptm) REVERT: E 103 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: E 178 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7847 (tpt170) REVERT: E 327 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7793 (ptt-90) REVERT: E 412 ASP cc_start: 0.8373 (p0) cc_final: 0.8162 (p0) REVERT: G 75 ILE cc_start: 0.8021 (pt) cc_final: 0.7782 (pp) REVERT: H 79 GLN cc_start: 0.4981 (OUTLIER) cc_final: 0.4274 (tp40) REVERT: L 79 GLN cc_start: 0.5189 (OUTLIER) cc_final: 0.4817 (tp40) outliers start: 59 outliers final: 25 residues processed: 284 average time/residue: 0.5604 time to fit residues: 180.8919 Evaluate side-chains 285 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 137 ASN B 653 GLN B 658 GLN C 136 ASN C 137 ASN C 422 GLN D 543 ASN D 611 ASN E 136 ASN E 137 ASN E 315 GLN G 76 ASN ** H 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN J 45 ASN K 76 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.175154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126320 restraints weight = 21505.840| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.94 r_work: 0.3318 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20466 Z= 0.197 Angle : 0.671 12.212 27948 Z= 0.329 Chirality : 0.046 0.274 3351 Planarity : 0.004 0.056 3402 Dihedral : 5.158 38.396 2558 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.31 % Allowed : 11.89 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.76 (0.18), residues: 2352 helix: 1.36 (0.27), residues: 387 sheet: 0.80 (0.18), residues: 771 loop : 0.12 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 178 TYR 0.015 0.002 TYR C 318 PHE 0.017 0.002 PHE A 383 TRP 0.017 0.002 TRP C 427 HIS 0.004 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (20337) covalent geometry : angle 0.62233 / 0.32 (27603) SS BOND : bond 0.00321 / 0.21 ( 42) SS BOND : angle 1.60871 / 1.11 ( 84) hydrogen bonds : bond 0.04419 / 3.03 ( 723) hydrogen bonds : angle 4.81031 / 3.34 ( 2070) link_ALPHA1-2 : bond 0.00256 / 0.12 ( 3) link_ALPHA1-2 : angle 1.53820 / 0.88 ( 9) link_ALPHA1-3 : bond 0.00227 / 0.10 ( 3) link_ALPHA1-3 : angle 1.35764 / 0.84 ( 9) link_BETA1-4 : bond 0.00433 / 0.29 ( 36) link_BETA1-4 : angle 1.51493 / 1.04 ( 108) link_NAG-ASN : bond 0.00442 / 0.28 ( 45) link_NAG-ASN : angle 3.19309 / 2.18 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 251 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8659 (t) REVERT: A 103 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: A 178 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7946 (tpt170) REVERT: A 501 CYS cc_start: 0.7590 (OUTLIER) cc_final: 0.6653 (p) REVERT: A 502 LYS cc_start: 0.7662 (ttpt) cc_final: 0.7202 (tttt) REVERT: B 530 MET cc_start: 0.8583 (mtp) cc_final: 0.8349 (mtp) REVERT: B 542 ARG cc_start: 0.8521 (mtp-110) cc_final: 0.7245 (mtt90) REVERT: B 632 ASP cc_start: 0.8498 (t70) cc_final: 0.8133 (t0) REVERT: B 655 LYS cc_start: 0.6888 (mtmt) cc_final: 0.5302 (pttt) REVERT: C 103 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: C 173 TYR cc_start: 0.8821 (p90) cc_final: 0.8606 (p90) REVERT: C 327 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7741 (ptt-90) REVERT: C 340 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7677 (pp20) REVERT: D 632 ASP cc_start: 0.8335 (t70) cc_final: 0.7871 (t0) REVERT: D 655 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6759 (mtpt) REVERT: E 95 MET cc_start: 0.8996 (ptm) cc_final: 0.8677 (ptm) REVERT: E 97 LYS cc_start: 0.8497 (mmpt) cc_final: 0.7883 (mptt) REVERT: E 103 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: E 178 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7833 (tpt170) REVERT: E 327 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7779 (ptt-90) REVERT: E 412 ASP cc_start: 0.8346 (p0) cc_final: 0.8101 (p0) REVERT: H 79 GLN cc_start: 0.4989 (OUTLIER) cc_final: 0.4306 (tp40) REVERT: L 79 GLN cc_start: 0.5181 (OUTLIER) cc_final: 0.4865 (tp40) outliers start: 69 outliers final: 31 residues processed: 296 average time/residue: 0.5656 time to fit residues: 191.2182 Evaluate side-chains 288 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 148 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 137 ASN B 658 GLN C 136 ASN C 137 ASN D 611 ASN E 136 ASN E 137 ASN E 315 GLN F 611 ASN F 651 ASN I 76 ASN K 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.175685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121859 restraints weight = 21532.612| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.08 r_work: 0.3341 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20466 Z= 0.188 Angle : 0.658 11.986 27948 Z= 0.323 Chirality : 0.045 0.271 3351 Planarity : 0.004 0.053 3402 Dihedral : 5.128 40.090 2558 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.65 % Allowed : 12.09 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.71 (0.17), residues: 2352 helix: 1.33 (0.27), residues: 390 sheet: 0.77 (0.18), residues: 771 loop : 0.07 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 178 TYR 0.014 0.002 TYR A 318 PHE 0.014 0.002 PHE A 383 TRP 0.018 0.002 TRP C 427 HIS 0.005 0.001 HIS H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (20337) covalent geometry : angle 0.61205 / 0.31 (27603) SS BOND : bond 0.00327 / 0.21 ( 42) SS BOND : angle 1.50909 / 1.04 ( 84) hydrogen bonds : bond 0.04310 / 2.97 ( 723) hydrogen bonds : angle 4.74779 / 3.30 ( 2070) link_ALPHA1-2 : bond 0.00291 / 0.13 ( 3) link_ALPHA1-2 : angle 1.49306 / 0.86 ( 9) link_ALPHA1-3 : bond 0.00236 / 0.10 ( 3) link_ALPHA1-3 : angle 1.36316 / 0.83 ( 9) link_BETA1-4 : bond 0.00424 / 0.28 ( 36) link_BETA1-4 : angle 1.44830 / 0.99 ( 108) link_NAG-ASN : bond 0.00420 / 0.27 ( 45) link_NAG-ASN : angle 3.08921 / 2.11 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 252 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 51 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8755 (t) REVERT: A 103 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: A 178 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7960 (tpt170) REVERT: A 502 LYS cc_start: 0.7552 (ttpt) cc_final: 0.7099 (tttt) REVERT: B 530 MET cc_start: 0.8628 (mtp) cc_final: 0.8403 (mtp) REVERT: B 542 ARG cc_start: 0.8534 (mtp-110) cc_final: 0.7322 (mtt90) REVERT: B 601 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8600 (mttt) REVERT: B 632 ASP cc_start: 0.8458 (t70) cc_final: 0.8050 (t0) REVERT: B 655 LYS cc_start: 0.6997 (mtmt) cc_final: 0.5391 (pttt) REVERT: C 103 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: C 327 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7813 (ptt-90) REVERT: C 340 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7720 (pp20) REVERT: D 632 ASP cc_start: 0.8333 (t70) cc_final: 0.7962 (t70) REVERT: E 95 MET cc_start: 0.9038 (ptm) cc_final: 0.8713 (ptm) REVERT: E 97 LYS cc_start: 0.8531 (mmpt) cc_final: 0.7967 (mptt) REVERT: E 103 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: E 178 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7828 (tpt170) REVERT: E 327 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7830 (ptt-90) REVERT: H 79 GLN cc_start: 0.4972 (OUTLIER) cc_final: 0.4425 (tp40) REVERT: L 79 GLN cc_start: 0.5163 (OUTLIER) cc_final: 0.4841 (tp40) REVERT: L 90 HIS cc_start: 0.6618 (OUTLIER) cc_final: 0.5367 (p-80) outliers start: 76 outliers final: 40 residues processed: 300 average time/residue: 0.5930 time to fit residues: 202.0951 Evaluate side-chains 294 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 242 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 90 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 86 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 137 ASN B 591 GLN B 658 GLN C 136 ASN C 137 ASN E 136 ASN E 137 ASN F 611 ASN G 76 ASN I 76 ASN K 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.175258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121479 restraints weight = 21321.360| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.06 r_work: 0.3334 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20466 Z= 0.197 Angle : 0.668 11.755 27948 Z= 0.328 Chirality : 0.046 0.271 3351 Planarity : 0.004 0.051 3402 Dihedral : 5.153 41.516 2558 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.69 % Allowed : 13.19 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.71 (0.17), residues: 2352 helix: 1.29 (0.27), residues: 390 sheet: 0.76 (0.18), residues: 771 loop : 0.09 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.015 0.002 TYR A 318 PHE 0.014 0.002 PHE A 383 TRP 0.018 0.002 TRP A 427 HIS 0.004 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (20337) covalent geometry : angle 0.62266 / 0.32 (27603) SS BOND : bond 0.00337 / 0.22 ( 42) SS BOND : angle 1.44750 / 1.00 ( 84) hydrogen bonds : bond 0.04385 / 3.02 ( 723) hydrogen bonds : angle 4.75274 / 3.30 ( 2070) link_ALPHA1-2 : bond 0.00257 / 0.11 ( 3) link_ALPHA1-2 : angle 1.52372 / 0.88 ( 9) link_ALPHA1-3 : bond 0.00215 / 0.09 ( 3) link_ALPHA1-3 : angle 1.36754 / 0.84 ( 9) link_BETA1-4 : bond 0.00415 / 0.28 ( 36) link_BETA1-4 : angle 1.46364 / 1.01 ( 108) link_NAG-ASN : bond 0.00444 / 0.28 ( 45) link_NAG-ASN : angle 3.11210 / 2.12 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 246 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 51 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8722 (t) REVERT: A 103 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: A 178 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7991 (tpt170) REVERT: A 501 CYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6568 (p) REVERT: A 502 LYS cc_start: 0.7619 (ttpt) cc_final: 0.7174 (tttt) REVERT: B 530 MET cc_start: 0.8620 (mtp) cc_final: 0.8380 (mtp) REVERT: B 542 ARG cc_start: 0.8520 (mtp-110) cc_final: 0.7242 (mtt90) REVERT: B 632 ASP cc_start: 0.8430 (t70) cc_final: 0.7983 (t0) REVERT: B 655 LYS cc_start: 0.6899 (mtmt) cc_final: 0.5298 (pttt) REVERT: C 66 HIS cc_start: 0.6253 (OUTLIER) cc_final: 0.5942 (m90) REVERT: C 103 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: C 327 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7745 (ptt-90) REVERT: C 340 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7643 (pp20) REVERT: D 632 ASP cc_start: 0.8371 (t70) cc_final: 0.8005 (t0) REVERT: D 658 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.6354 (tt0) REVERT: E 95 MET cc_start: 0.9034 (ptm) cc_final: 0.8712 (ptm) REVERT: E 97 LYS cc_start: 0.8500 (mmpt) cc_final: 0.7927 (mptt) REVERT: E 103 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: E 178 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7823 (tpt170) REVERT: E 327 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7763 (ptt-90) REVERT: H 79 GLN cc_start: 0.5029 (OUTLIER) cc_final: 0.4557 (tp40) REVERT: H 90 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.5043 (p-80) REVERT: L 79 GLN cc_start: 0.5049 (OUTLIER) cc_final: 0.4727 (tp40) REVERT: L 90 HIS cc_start: 0.6714 (OUTLIER) cc_final: 0.5388 (p-80) outliers start: 77 outliers final: 39 residues processed: 294 average time/residue: 0.6039 time to fit residues: 202.1708 Evaluate side-chains 297 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 90 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 173 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 137 ASN B 658 GLN C 136 ASN C 137 ASN E 136 ASN E 137 ASN F 611 ASN F 651 ASN G 76 ASN I 76 ASN K 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.176925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123420 restraints weight = 21483.094| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.07 r_work: 0.3366 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20466 Z= 0.134 Angle : 0.600 10.896 27948 Z= 0.297 Chirality : 0.043 0.263 3351 Planarity : 0.004 0.050 3402 Dihedral : 4.910 40.712 2558 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.07 % Allowed : 14.24 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.85 (0.18), residues: 2352 helix: 1.49 (0.27), residues: 390 sheet: 0.84 (0.18), residues: 762 loop : 0.17 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 30 TYR 0.012 0.001 TYR A 318 PHE 0.013 0.001 PHE A 383 TRP 0.017 0.001 TRP A 427 HIS 0.004 0.001 HIS L 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (20337) covalent geometry : angle 0.55891 / 0.29 (27603) SS BOND : bond 0.00301 / 0.18 ( 42) SS BOND : angle 1.36991 / 0.94 ( 84) hydrogen bonds : bond 0.03870 / 2.65 ( 723) hydrogen bonds : angle 4.63341 / 3.22 ( 2070) link_ALPHA1-2 : bond 0.00318 / 0.14 ( 3) link_ALPHA1-2 : angle 1.45477 / 0.84 ( 9) link_ALPHA1-3 : bond 0.00331 / 0.15 ( 3) link_ALPHA1-3 : angle 1.32698 / 0.80 ( 9) link_BETA1-4 : bond 0.00419 / 0.28 ( 36) link_BETA1-4 : angle 1.33573 / 0.91 ( 108) link_NAG-ASN : bond 0.00315 / 0.20 ( 45) link_NAG-ASN : angle 2.81279 / 1.93 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 251 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: B 530 MET cc_start: 0.8632 (mtp) cc_final: 0.8426 (mtp) REVERT: B 542 ARG cc_start: 0.8547 (mtp-110) cc_final: 0.7310 (mtt90) REVERT: B 632 ASP cc_start: 0.8443 (t70) cc_final: 0.8010 (t0) REVERT: B 655 LYS cc_start: 0.6901 (mtmt) cc_final: 0.5268 (pttt) REVERT: C 66 HIS cc_start: 0.6262 (OUTLIER) cc_final: 0.5952 (m90) REVERT: C 103 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: C 327 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7743 (ptt-90) REVERT: C 340 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7640 (pp20) REVERT: D 632 ASP cc_start: 0.8343 (t70) cc_final: 0.8002 (t0) REVERT: D 658 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6338 (tt0) REVERT: E 95 MET cc_start: 0.9033 (ptm) cc_final: 0.8679 (ptm) REVERT: E 97 LYS cc_start: 0.8504 (mmpt) cc_final: 0.7961 (mptt) REVERT: E 178 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7793 (tpt170) REVERT: E 327 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7804 (ptt-90) REVERT: H 79 GLN cc_start: 0.5098 (OUTLIER) cc_final: 0.4608 (tp40) REVERT: L 42 LYS cc_start: 0.6682 (OUTLIER) cc_final: 0.6279 (tttm) REVERT: L 79 GLN cc_start: 0.5136 (OUTLIER) cc_final: 0.4890 (tp40) REVERT: L 90 HIS cc_start: 0.6717 (OUTLIER) cc_final: 0.5474 (p-80) outliers start: 64 outliers final: 33 residues processed: 294 average time/residue: 0.6228 time to fit residues: 207.7299 Evaluate side-chains 284 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 90 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 101 optimal weight: 5.9990 chunk 147 optimal weight: 0.0970 chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 121 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN D 651 ASN E 136 ASN E 137 ASN F 611 ASN F 651 ASN G 76 ASN I 76 ASN K 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.176856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123219 restraints weight = 21535.911| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.07 r_work: 0.3361 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20466 Z= 0.143 Angle : 0.605 10.361 27948 Z= 0.299 Chirality : 0.044 0.262 3351 Planarity : 0.004 0.049 3402 Dihedral : 4.892 40.173 2558 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.02 % Allowed : 14.20 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.87 (0.18), residues: 2352 helix: 1.51 (0.27), residues: 390 sheet: 0.84 (0.18), residues: 762 loop : 0.19 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.012 0.001 TYR A 318 PHE 0.013 0.001 PHE C 383 TRP 0.015 0.002 TRP I 50 HIS 0.007 0.001 HIS H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (20337) covalent geometry : angle 0.56460 / 0.29 (27603) SS BOND : bond 0.00249 / 0.16 ( 42) SS BOND : angle 1.32337 / 0.91 ( 84) hydrogen bonds : bond 0.03887 / 2.67 ( 723) hydrogen bonds : angle 4.60573 / 3.21 ( 2070) link_ALPHA1-2 : bond 0.00328 / 0.14 ( 3) link_ALPHA1-2 : angle 1.48351 / 0.86 ( 9) link_ALPHA1-3 : bond 0.00314 / 0.14 ( 3) link_ALPHA1-3 : angle 1.32460 / 0.80 ( 9) link_BETA1-4 : bond 0.00412 / 0.27 ( 36) link_BETA1-4 : angle 1.34550 / 0.92 ( 108) link_NAG-ASN : bond 0.00327 / 0.21 ( 45) link_NAG-ASN : angle 2.78846 / 1.91 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 247 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: B 530 MET cc_start: 0.8645 (mtp) cc_final: 0.8438 (mtp) REVERT: B 542 ARG cc_start: 0.8556 (mtp-110) cc_final: 0.7364 (mtt90) REVERT: B 632 ASP cc_start: 0.8432 (t70) cc_final: 0.8010 (t0) REVERT: B 655 LYS cc_start: 0.6904 (mtmt) cc_final: 0.5317 (pttt) REVERT: C 103 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: C 327 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7782 (ptt-90) REVERT: C 340 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7692 (pp20) REVERT: C 499 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7893 (p) REVERT: D 632 ASP cc_start: 0.8362 (t70) cc_final: 0.8030 (t0) REVERT: D 658 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6391 (tt0) REVERT: E 95 MET cc_start: 0.9044 (ptm) cc_final: 0.8717 (ptm) REVERT: E 103 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: E 178 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7809 (tpt170) REVERT: E 327 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7855 (ptt-90) REVERT: H 79 GLN cc_start: 0.5135 (OUTLIER) cc_final: 0.4627 (tp40) REVERT: H 90 HIS cc_start: 0.6603 (OUTLIER) cc_final: 0.5074 (p-80) REVERT: J 20 THR cc_start: 0.7181 (m) cc_final: 0.6688 (p) REVERT: L 79 GLN cc_start: 0.5164 (OUTLIER) cc_final: 0.4920 (tp40) REVERT: L 90 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.5579 (p-80) outliers start: 63 outliers final: 38 residues processed: 288 average time/residue: 0.6096 time to fit residues: 199.9885 Evaluate side-chains 289 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 90 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 139 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 222 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 137 ASN D 651 ASN E 136 ASN E 137 ASN E 352 HIS F 611 ASN F 651 ASN I 76 ASN L 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.175719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121964 restraints weight = 21293.915| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.05 r_work: 0.3347 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20466 Z= 0.184 Angle : 0.651 10.977 27948 Z= 0.320 Chirality : 0.045 0.266 3351 Planarity : 0.004 0.079 3402 Dihedral : 5.057 41.181 2558 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.93 % Allowed : 14.48 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.72 (0.17), residues: 2352 helix: 1.07 (0.27), residues: 408 sheet: 0.79 (0.18), residues: 762 loop : 0.16 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.014 0.002 TYR A 318 PHE 0.016 0.002 PHE A 383 TRP 0.020 0.002 TRP I 50 HIS 0.007 0.001 HIS H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (20337) covalent geometry : angle 0.60846 / 0.31 (27603) SS BOND : bond 0.00305 / 0.20 ( 42) SS BOND : angle 1.42110 / 0.98 ( 84) hydrogen bonds : bond 0.04219 / 2.91 ( 723) hydrogen bonds : angle 4.69379 / 3.27 ( 2070) link_ALPHA1-2 : bond 0.00287 / 0.13 ( 3) link_ALPHA1-2 : angle 1.52175 / 0.88 ( 9) link_ALPHA1-3 : bond 0.00245 / 0.11 ( 3) link_ALPHA1-3 : angle 1.35448 / 0.83 ( 9) link_BETA1-4 : bond 0.00410 / 0.27 ( 36) link_BETA1-4 : angle 1.41293 / 0.97 ( 108) link_NAG-ASN : bond 0.00419 / 0.27 ( 45) link_NAG-ASN : angle 2.98945 / 2.04 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 240 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: B 530 MET cc_start: 0.8629 (mtp) cc_final: 0.8388 (mtp) REVERT: B 542 ARG cc_start: 0.8602 (mtp-110) cc_final: 0.7338 (mtt90) REVERT: B 632 ASP cc_start: 0.8429 (t70) cc_final: 0.8001 (t0) REVERT: B 655 LYS cc_start: 0.6923 (mtmt) cc_final: 0.5303 (pttt) REVERT: C 103 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: C 327 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7733 (ptt-90) REVERT: C 340 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7673 (pp20) REVERT: D 632 ASP cc_start: 0.8348 (t70) cc_final: 0.8016 (t0) REVERT: D 658 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6366 (tt0) REVERT: E 95 MET cc_start: 0.9055 (ptm) cc_final: 0.8685 (ptm) REVERT: E 103 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: E 178 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7837 (tpt170) REVERT: E 327 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7777 (ptt-90) REVERT: H 79 GLN cc_start: 0.5112 (OUTLIER) cc_final: 0.4623 (tp40) REVERT: H 90 HIS cc_start: 0.6681 (OUTLIER) cc_final: 0.5217 (p-80) REVERT: L 79 GLN cc_start: 0.5160 (OUTLIER) cc_final: 0.4869 (tp40) REVERT: L 90 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.5616 (p-80) outliers start: 61 outliers final: 38 residues processed: 281 average time/residue: 0.6224 time to fit residues: 198.6759 Evaluate side-chains 287 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 658 GLN Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 90 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 207 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 187 optimal weight: 0.0980 chunk 201 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 199 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 154 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN B 658 GLN C 136 ASN C 137 ASN E 136 ASN E 137 ASN F 611 ASN F 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.177807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124367 restraints weight = 21421.939| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.07 r_work: 0.3378 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20466 Z= 0.120 Angle : 0.582 9.982 27948 Z= 0.289 Chirality : 0.043 0.259 3351 Planarity : 0.004 0.070 3402 Dihedral : 4.788 39.892 2558 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.30 % Allowed : 15.11 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.85 (0.18), residues: 2352 helix: 1.25 (0.27), residues: 408 sheet: 0.90 (0.18), residues: 756 loop : 0.19 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 30 TYR 0.012 0.001 TYR D 638 PHE 0.012 0.001 PHE E 53 TRP 0.020 0.001 TRP I 50 HIS 0.007 0.001 HIS H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (20337) covalent geometry : angle 0.54442 / 0.28 (27603) SS BOND : bond 0.00221 / 0.15 ( 42) SS BOND : angle 1.18766 / 0.83 ( 84) hydrogen bonds : bond 0.03640 / 2.49 ( 723) hydrogen bonds : angle 4.59086 / 3.20 ( 2070) link_ALPHA1-2 : bond 0.00328 / 0.14 ( 3) link_ALPHA1-2 : angle 1.44132 / 0.84 ( 9) link_ALPHA1-3 : bond 0.00364 / 0.16 ( 3) link_ALPHA1-3 : angle 1.31001 / 0.78 ( 9) link_BETA1-4 : bond 0.00420 / 0.27 ( 36) link_BETA1-4 : angle 1.27050 / 0.87 ( 108) link_NAG-ASN : bond 0.00270 / 0.17 ( 45) link_NAG-ASN : angle 2.66318 / 1.83 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: B 530 MET cc_start: 0.8619 (mtp) cc_final: 0.8406 (mtp) REVERT: B 542 ARG cc_start: 0.8591 (mtp-110) cc_final: 0.7335 (mtt90) REVERT: B 632 ASP cc_start: 0.8406 (t70) cc_final: 0.7991 (t0) REVERT: B 655 LYS cc_start: 0.6833 (mtmt) cc_final: 0.5261 (pttt) REVERT: C 103 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: C 327 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7703 (ptt-90) REVERT: C 340 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7624 (pp20) REVERT: D 632 ASP cc_start: 0.8325 (t70) cc_final: 0.8012 (t0) REVERT: E 95 MET cc_start: 0.9028 (ptm) cc_final: 0.8685 (ptm) REVERT: E 178 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7769 (tpt170) REVERT: E 327 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7739 (ptt-90) REVERT: H 79 GLN cc_start: 0.5196 (OUTLIER) cc_final: 0.4740 (tp40) REVERT: H 90 HIS cc_start: 0.6591 (OUTLIER) cc_final: 0.5104 (p-80) REVERT: L 20 THR cc_start: 0.7204 (m) cc_final: 0.6739 (p) REVERT: L 79 GLN cc_start: 0.5191 (OUTLIER) cc_final: 0.4953 (tp40) REVERT: L 90 HIS cc_start: 0.6691 (OUTLIER) cc_final: 0.5684 (p-80) outliers start: 48 outliers final: 29 residues processed: 270 average time/residue: 0.6429 time to fit residues: 196.3619 Evaluate side-chains 273 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 327 ARG Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 90 HIS Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 90 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 175 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 137 ASN C 136 ASN C 137 ASN D 651 ASN E 136 ASN E 137 ASN F 651 ASN K 76 ASN L 6 GLN L 70 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.176395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122546 restraints weight = 21360.052| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.06 r_work: 0.3355 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20466 Z= 0.165 Angle : 0.630 11.016 27948 Z= 0.311 Chirality : 0.044 0.262 3351 Planarity : 0.004 0.067 3402 Dihedral : 4.945 40.277 2558 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.21 % Allowed : 15.35 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.78 (0.18), residues: 2352 helix: 1.15 (0.27), residues: 408 sheet: 0.87 (0.18), residues: 756 loop : 0.16 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 585 TYR 0.013 0.002 TYR A 318 PHE 0.015 0.002 PHE A 383 TRP 0.023 0.002 TRP I 50 HIS 0.006 0.001 HIS H 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (20337) covalent geometry : angle 0.58973 / 0.30 (27603) SS BOND : bond 0.00272 / 0.17 ( 42) SS BOND : angle 1.44630 / 1.01 ( 84) hydrogen bonds : bond 0.04027 / 2.77 ( 723) hydrogen bonds : angle 4.65241 / 3.24 ( 2070) link_ALPHA1-2 : bond 0.00300 / 0.13 ( 3) link_ALPHA1-2 : angle 1.50812 / 0.87 ( 9) link_ALPHA1-3 : bond 0.00275 / 0.12 ( 3) link_ALPHA1-3 : angle 1.33611 / 0.82 ( 9) link_BETA1-4 : bond 0.00405 / 0.27 ( 36) link_BETA1-4 : angle 1.36498 / 0.94 ( 108) link_NAG-ASN : bond 0.00373 / 0.24 ( 45) link_NAG-ASN : angle 2.85046 / 1.95 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8498.96 seconds wall clock time: 145 minutes 31.77 seconds (8731.77 seconds total)