Starting phenix.real_space_refine on Thu Mar 5 07:16:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6orp_20177/03_2026/6orp_20177.cif Found real_map, /net/cci-nas-00/data/ceres_data/6orp_20177/03_2026/6orp_20177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6orp_20177/03_2026/6orp_20177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6orp_20177/03_2026/6orp_20177.map" model { file = "/net/cci-nas-00/data/ceres_data/6orp_20177/03_2026/6orp_20177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6orp_20177/03_2026/6orp_20177.cif" } resolution = 4.4 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= -0.002 sd= 0.204 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 114 5.16 5 C 12487 2.51 5 N 3317 2.21 5 O 4054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19972 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "I" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "J" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "K" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.21, per 1000 atoms: 0.26 Number of scatterers: 19972 At special positions: 0 Unit cell: (139.292, 133.548, 150.78, 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 114 16.00 O 4054 8.00 N 3317 7.00 C 12487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS B 501 " distance=2.05 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.05 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.07 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.05 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.06 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.05 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.02 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.09 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.09 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " 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 ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA b 3 " - " MAN b 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA j 3 " - " MAN j 5 " 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 P 2 " - " BMA P 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG 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 g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " 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-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 601 " - " ASN B 88 " " NAG B 614 " - " ASN B 295 " " NAG B 620 " - " ASN B 339 " " NAG B 621 " - " ASN B 355 " " NAG C 703 " - " ASN C 618 " " NAG C 704 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 615 " - " ASN G 295 " " NAG G 620 " - " ASN G 339 " " NAG G 621 " - " ASN G 355 " " NAG G 622 " - " ASN G 392 " " NAG G 627 " - " ASN G 448 " " NAG I 601 " - " ASN I 88 " " NAG I 619 " - " ASN I 295 " " NAG I 625 " - " ASN I 339 " " NAG I 626 " - " ASN I 355 " " NAG I 631 " - " ASN I 448 " " NAG M 1 " - " ASN B 160 " " NAG N 1 " - " ASN B 197 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 262 " " NAG Q 1 " - " ASN B 301 " " NAG R 1 " - " ASN B 332 " " NAG S 1 " - " ASN B 386 " " NAG T 1 " - " ASN B 448 " " NAG U 1 " - " ASN B 392 " " NAG V 1 " - " ASN B 276 " " NAG W 1 " - " ASN C 611 " " NAG X 1 " - " ASN G 88 " " NAG Y 1 " - " ASN G 160 " " NAG Z 1 " - " ASN G 197 " " NAG a 1 " - " ASN G 234 " " NAG b 1 " - " ASN G 262 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 279 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN I 160 " " NAG h 1 " - " ASN I 197 " " NAG i 1 " - " ASN I 234 " " NAG j 1 " - " ASN I 262 " " NAG k 1 " - " ASN I 279 " " NAG l 1 " - " ASN I 301 " " NAG m 1 " - " ASN I 332 " " NAG n 1 " - " ASN I 386 " " NAG o 1 " - " ASN I 392 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4422 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 43 sheets defined 16.8% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 543 removed outlier: 3.666A pdb=" N ALA A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.579A pdb=" N VAL A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.611A pdb=" N ILE A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 removed outlier: 3.502A pdb=" N ASP A 632 " --> pdb=" O TRP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 648 removed outlier: 3.696A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.782A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.602A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 removed outlier: 4.208A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 546 removed outlier: 3.695A pdb=" N ALA C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 546 " --> pdb=" O ARG C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.641A pdb=" N VAL C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 632 removed outlier: 3.618A pdb=" N ASP C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 649 removed outlier: 4.967A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 661 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.760A pdb=" N SER D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER D 32 " --> pdb=" O ILE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'E' and resid 26 through 29 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.764A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 595 removed outlier: 4.415A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.595A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 632 Processing helix chain 'F' and resid 638 through 648 removed outlier: 4.451A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 661 Processing helix chain 'G' and resid 99 through 116 removed outlier: 3.641A pdb=" N GLN G 103 " --> pdb=" O ASN G 99 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.634A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.722A pdb=" N ARG G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 476 through 481' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.761A pdb=" N SER H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.618A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 351 through 353 No H-bonds generated for 'chain 'I' and resid 351 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.557A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 481 removed outlier: 3.830A pdb=" N ARG I 480 " --> pdb=" O ARG I 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.760A pdb=" N SER J 31 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER J 32 " --> pdb=" O ILE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'K' and resid 26 through 29 Processing helix chain 'L' and resid 26 through 29 Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 46 removed outlier: 9.153A pdb=" N ILE B 491 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TRP B 45 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N VAL B 489 " --> pdb=" O TRP B 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 76 removed outlier: 4.360A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 176 removed outlier: 3.734A pdb=" N VAL B 172 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 159 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS B 131 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 189 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU B 190 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.249A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.130A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.511A pdb=" N ILE B 271 " --> pdb=" O GLN B 287 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 452 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.903A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 334 removed outlier: 3.785A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 8 removed outlier: 3.621A pdb=" N GLY D 8 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR D 21 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 17 through 18 removed outlier: 3.884A pdb=" N THR D 69 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 49 removed outlier: 4.514A pdb=" N TRP D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 19 through 24 removed outlier: 4.042A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 90 through 92 removed outlier: 3.644A pdb=" N ALA E 95B" --> pdb=" O ASP E 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 35 through 46 removed outlier: 3.540A pdb=" N GLY G 495 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N ILE G 491 " --> pdb=" O PRO G 43 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TRP G 45 " --> pdb=" O VAL G 489 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N VAL G 489 " --> pdb=" O TRP G 45 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 75 through 76 removed outlier: 4.458A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 92 through 94 removed outlier: 4.142A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 169 through 176 removed outlier: 3.923A pdb=" N VAL G 172 " --> pdb=" O PHE G 159 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE G 159 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS G 131 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.269A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 256 through 257 Processing sheet with id=AC2, first strand: chain 'G' and resid 259 through 260 removed outlier: 3.728A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 259 through 260 removed outlier: 6.589A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 383 through 385 removed outlier: 3.756A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 383 through 385 removed outlier: 3.756A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 304 through 307 removed outlier: 3.576A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.620A pdb=" N GLY H 8 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR H 21 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 17 through 18 removed outlier: 3.884A pdb=" N THR H 69 " --> pdb=" O LYS H 82 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 47 through 49 removed outlier: 4.514A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 35 through 46 removed outlier: 9.239A pdb=" N ILE I 491 " --> pdb=" O PRO I 43 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N TRP I 45 " --> pdb=" O VAL I 489 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N VAL I 489 " --> pdb=" O TRP I 45 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 53 through 55 removed outlier: 5.853A pdb=" N ILE I 215 " --> pdb=" O GLY I 250 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY I 250 " --> pdb=" O ILE I 215 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR I 217 " --> pdb=" O THR I 248 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 92 through 94 removed outlier: 4.139A pdb=" N GLY I 237 " --> pdb=" O PHE I 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 169 through 176 removed outlier: 3.840A pdb=" N PHE I 159 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS I 131 " --> pdb=" O LYS I 189 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 202 through 203 removed outlier: 5.852A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.823A pdb=" N ILE I 271 " --> pdb=" O GLN I 287 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 383 through 385 removed outlier: 3.673A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 383 through 385 removed outlier: 3.673A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR I 297 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 301 through 308 removed outlier: 7.656A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 6 through 8 removed outlier: 3.620A pdb=" N GLY J 8 " --> pdb=" O THR J 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR J 21 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 17 through 18 removed outlier: 3.884A pdb=" N THR J 69 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 47 through 49 removed outlier: 4.513A pdb=" N TRP J 37 " --> pdb=" O ILE J 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.042A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 90 through 92 removed outlier: 3.646A pdb=" N ALA K 95B" --> pdb=" O ASP K 92 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.042A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 90 through 92 removed outlier: 3.645A pdb=" N ALA L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3206 1.31 - 1.45: 6838 1.45 - 1.59: 10176 1.59 - 1.73: 1 1.73 - 1.87: 150 Bond restraints: 20371 Sorted by residual: bond pdb=" C4 NAG e 1 " pdb=" O4 NAG e 1 " ideal model delta sigma weight residual 1.409 1.524 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C7 NAG B 614 " pdb=" N2 NAG B 614 " ideal model delta sigma weight residual 1.346 1.243 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C1 NAG B 614 " pdb=" C2 NAG B 614 " ideal model delta sigma weight residual 1.532 1.434 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C2 NAG B 614 " pdb=" N2 NAG B 614 " ideal model delta sigma weight residual 1.439 1.342 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C3 NAG B 614 " pdb=" C4 NAG B 614 " ideal model delta sigma weight residual 1.524 1.432 0.092 2.00e-02 2.50e+03 2.12e+01 ... (remaining 20366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 27250 5.28 - 10.56: 362 10.56 - 15.84: 48 15.84 - 21.12: 10 21.12 - 26.40: 4 Bond angle restraints: 27674 Sorted by residual: angle pdb=" CA ASN G 448 " pdb=" C ASN G 448 " pdb=" O ASN G 448 " ideal model delta sigma weight residual 119.32 104.70 14.62 1.19e+00 7.06e-01 1.51e+02 angle pdb=" C ASN G 448 " pdb=" N ILE G 449 " pdb=" CA ILE G 449 " ideal model delta sigma weight residual 121.97 140.56 -18.59 1.80e+00 3.09e-01 1.07e+02 angle pdb=" O SER G 447 " pdb=" C SER G 447 " pdb=" N ASN G 448 " ideal model delta sigma weight residual 123.10 133.55 -10.45 1.15e+00 7.56e-01 8.26e+01 angle pdb=" C3 NAG C 704 " pdb=" C2 NAG C 704 " pdb=" N2 NAG C 704 " ideal model delta sigma weight residual 110.74 84.34 26.40 3.00e+00 1.11e-01 7.75e+01 angle pdb=" C1 NAG j 1 " pdb=" C2 NAG j 1 " pdb=" N2 NAG j 1 " ideal model delta sigma weight residual 110.79 88.76 22.03 3.00e+00 1.11e-01 5.39e+01 ... (remaining 27669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 12278 22.45 - 44.91: 814 44.91 - 67.36: 155 67.36 - 89.81: 105 89.81 - 112.26: 55 Dihedral angle restraints: 13407 sinusoidal: 6537 harmonic: 6870 Sorted by residual: dihedral pdb=" CB CYS F 605 " pdb=" SG CYS F 605 " pdb=" SG CYS I 501 " pdb=" CB CYS I 501 " ideal model delta sinusoidal sigma weight residual -86.00 2.89 -88.89 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CA GLN K 34 " pdb=" C GLN K 34 " pdb=" N TRP K 35 " pdb=" CA TRP K 35 " ideal model delta harmonic sigma weight residual 180.00 134.99 45.01 0 5.00e+00 4.00e-02 8.10e+01 dihedral pdb=" CA GLN L 34 " pdb=" C GLN L 34 " pdb=" N TRP L 35 " pdb=" CA TRP L 35 " ideal model delta harmonic sigma weight residual 180.00 135.03 44.97 0 5.00e+00 4.00e-02 8.09e+01 ... (remaining 13404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.241: 3307 0.241 - 0.483: 73 0.483 - 0.724: 5 0.724 - 0.965: 2 0.965 - 1.207: 4 Chirality restraints: 3391 Sorted by residual: chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.81 0.41 2.00e-02 2.50e+03 4.13e+02 chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-02 2.50e+03 2.63e+02 chirality pdb=" C1 NAG j 2 " pdb=" O4 NAG j 1 " pdb=" C2 NAG j 2 " pdb=" O5 NAG j 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.54e+02 ... (remaining 3388 not shown) Planarity restraints: 3440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 1 " -0.366 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG f 1 " 0.096 2.00e-02 2.50e+03 pdb=" C8 NAG f 1 " -0.192 2.00e-02 2.50e+03 pdb=" N2 NAG f 1 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG f 1 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 2 " 0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG U 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG U 2 " 0.100 2.00e-02 2.50e+03 pdb=" N2 NAG U 2 " -0.529 2.00e-02 2.50e+03 pdb=" O7 NAG U 2 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.336 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG j 1 " 0.120 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.499 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.104 2.00e-02 2.50e+03 ... (remaining 3437 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 15 2.21 - 2.88: 7971 2.88 - 3.56: 27575 3.56 - 4.23: 44211 4.23 - 4.90: 67651 Nonbonded interactions: 147423 Sorted by model distance: nonbonded pdb=" CE2 PHE B 391 " pdb=" CG PRO B 470 " model vdw 1.539 3.740 nonbonded pdb=" CE3 TRP G 96 " pdb=" OE2 GLU G 275 " model vdw 1.863 3.340 nonbonded pdb=" CE2 PHE B 391 " pdb=" CB PRO B 470 " model vdw 1.868 3.740 nonbonded pdb=" O4 NAG C 704 " pdb=" O6 NAG C 704 " model vdw 1.983 3.040 nonbonded pdb=" O4 NAG A 703 " pdb=" O6 NAG A 703 " model vdw 1.998 3.040 ... (remaining 147418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 518 through 702) selection = chain 'C' selection = (chain 'F' and resid 518 through 702) } ncs_group { reference = chain 'B' selection = (chain 'G' and resid 31 through 622) selection = (chain 'I' and resid 31 through 626) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'l' selection = chain 'n' selection = chain 'o' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'm' } ncs_group { reference = chain 'P' selection = chain 'j' } 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 group one per residue 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: 1.130 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.410 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 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 : 0.010 0.115 20499 Z= 0.485 Angle : 1.752 26.404 28028 Z= 0.845 Chirality : 0.099 1.207 3391 Planarity : 0.015 0.306 3389 Dihedral : 18.024 112.263 8895 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.43 % Allowed : 15.83 % Favored : 83.74 % Rotamer: Outliers : 1.05 % Allowed : 8.24 % Favored : 90.71 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 1.59 % 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: -4.88 (0.14), residues: 2343 helix: -3.44 (0.19), residues: 333 sheet: -2.48 (0.19), residues: 564 loop : -3.71 (0.14), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 429 TYR 0.073 0.004 TYR B 173 PHE 0.033 0.004 PHE B 320 TRP 0.036 0.005 TRP H 100B HIS 0.021 0.003 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00964 (20371) covalent geometry : angle 1.62168 (27674) SS BOND : bond 0.01905 ( 30) SS BOND : angle 3.09748 ( 60) hydrogen bonds : bond 0.22160 ( 451) hydrogen bonds : angle 10.22535 ( 1239) link_ALPHA1-3 : bond 0.01473 ( 3) link_ALPHA1-3 : angle 4.22306 ( 9) link_ALPHA1-6 : bond 0.00717 ( 2) link_ALPHA1-6 : angle 2.29520 ( 6) link_BETA1-4 : bond 0.01917 ( 42) link_BETA1-4 : angle 6.75584 ( 126) link_NAG-ASN : bond 0.02066 ( 51) link_NAG-ASN : angle 6.64536 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 896 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 LEU cc_start: 0.8845 (mt) cc_final: 0.8627 (mt) REVERT: A 534 SER cc_start: 0.8967 (p) cc_final: 0.8602 (p) REVERT: A 543 ASN cc_start: 0.8175 (t0) cc_final: 0.7759 (t0) REVERT: A 624 ASP cc_start: 0.8398 (m-30) cc_final: 0.8198 (m-30) REVERT: B 97 LYS cc_start: 0.8313 (mmtp) cc_final: 0.8066 (mmmm) REVERT: B 116 LEU cc_start: 0.7173 (pp) cc_final: 0.6712 (pp) REVERT: B 131 CYS cc_start: 0.5986 (t) cc_final: 0.5698 (t) REVERT: B 150 MET cc_start: 0.7943 (mpp) cc_final: 0.7681 (mpp) REVERT: B 181 VAL cc_start: 0.7815 (t) cc_final: 0.7579 (t) REVERT: B 265 LEU cc_start: 0.8160 (mt) cc_final: 0.7825 (mm) REVERT: B 269 GLU cc_start: 0.8504 (tp30) cc_final: 0.8261 (tp30) REVERT: B 289 ASN cc_start: 0.8274 (p0) cc_final: 0.8045 (p0) REVERT: B 307 ILE cc_start: 0.7410 (mm) cc_final: 0.7120 (tp) REVERT: B 474 ASP cc_start: 0.7988 (t70) cc_final: 0.6688 (t0) REVERT: B 485 LYS cc_start: 0.6351 (ptpt) cc_final: 0.6107 (ptpp) REVERT: C 534 SER cc_start: 0.8972 (p) cc_final: 0.8582 (p) REVERT: C 543 ASN cc_start: 0.7901 (t0) cc_final: 0.7693 (t0) REVERT: C 583 VAL cc_start: 0.6947 (m) cc_final: 0.6677 (m) REVERT: C 624 ASP cc_start: 0.8131 (m-30) cc_final: 0.7794 (m-30) REVERT: C 658 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8272 (tp-100) REVERT: E 58 LEU cc_start: 0.7936 (tp) cc_final: 0.7497 (tp) REVERT: E 60 ASP cc_start: 0.6980 (t0) cc_final: 0.6147 (t0) REVERT: E 92 ASP cc_start: 0.7970 (t0) cc_final: 0.7703 (m-30) REVERT: F 522 PHE cc_start: 0.7390 (t80) cc_final: 0.6343 (t80) REVERT: F 534 SER cc_start: 0.8840 (p) cc_final: 0.8476 (p) REVERT: F 543 ASN cc_start: 0.7950 (t0) cc_final: 0.7700 (t0) REVERT: F 590 GLN cc_start: 0.8423 (tp-100) cc_final: 0.8180 (tm-30) REVERT: F 624 ASP cc_start: 0.8025 (m-30) cc_final: 0.7739 (m-30) REVERT: G 82 GLN cc_start: 0.8764 (mm-40) cc_final: 0.7937 (mp10) REVERT: G 94 ASN cc_start: 0.7961 (t0) cc_final: 0.7542 (t0) REVERT: G 98 ASN cc_start: 0.8262 (t0) cc_final: 0.8033 (t0) REVERT: G 171 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7576 (mtmt) REVERT: G 203 GLN cc_start: 0.7278 (pp30) cc_final: 0.6736 (pp30) REVERT: G 230 ASP cc_start: 0.8519 (t0) cc_final: 0.7990 (p0) REVERT: G 239 CYS cc_start: 0.5349 (t) cc_final: 0.5060 (t) REVERT: G 269 GLU cc_start: 0.8300 (tp30) cc_final: 0.7882 (tp30) REVERT: G 289 ASN cc_start: 0.8341 (p0) cc_final: 0.7920 (p0) REVERT: G 320 PHE cc_start: 0.8099 (t80) cc_final: 0.7384 (t80) REVERT: G 321 ASP cc_start: 0.7970 (m-30) cc_final: 0.7731 (m-30) REVERT: G 328 MET cc_start: 0.7465 (ptm) cc_final: 0.7044 (pmm) REVERT: G 369 LEU cc_start: 0.8293 (pp) cc_final: 0.8021 (mm) REVERT: G 426 MET cc_start: 0.7626 (ptt) cc_final: 0.7313 (ptm) REVERT: G 474 ASP cc_start: 0.7070 (t70) cc_final: 0.6542 (t70) REVERT: G 478 ASN cc_start: 0.6955 (m110) cc_final: 0.6556 (m110) REVERT: G 488 VAL cc_start: 0.5941 (p) cc_final: 0.5301 (p) REVERT: H 57 ASN cc_start: 0.6348 (t0) cc_final: 0.6066 (t0) REVERT: I 50 THR cc_start: 0.9334 (p) cc_final: 0.8962 (p) REVERT: I 53 PHE cc_start: 0.6691 (p90) cc_final: 0.6394 (p90) REVERT: I 87 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6672 (tm-30) REVERT: I 97 LYS cc_start: 0.8596 (mmtp) cc_final: 0.8260 (mmmm) REVERT: I 171 LYS cc_start: 0.8170 (pmmt) cc_final: 0.7560 (ptmt) REVERT: I 172 VAL cc_start: 0.8136 (p) cc_final: 0.7845 (p) REVERT: I 261 LEU cc_start: 0.7152 (tp) cc_final: 0.6906 (tp) REVERT: I 269 GLU cc_start: 0.8282 (tp30) cc_final: 0.8069 (tp30) REVERT: I 278 THR cc_start: 0.9055 (m) cc_final: 0.8830 (t) REVERT: I 289 ASN cc_start: 0.8238 (p0) cc_final: 0.7674 (p0) REVERT: I 308 ARG cc_start: 0.7783 (mpp80) cc_final: 0.7351 (mtm-85) REVERT: I 383 PHE cc_start: 0.6136 (m-10) cc_final: 0.5810 (m-10) REVERT: I 443 ILE cc_start: 0.8020 (mm) cc_final: 0.7788 (mp) REVERT: J 9 PRO cc_start: 0.8372 (Cg_endo) cc_final: 0.8110 (Cg_exo) REVERT: J 78 GLN cc_start: 0.7794 (mp10) cc_final: 0.7460 (mp10) REVERT: J 91 TYR cc_start: 0.7187 (m-80) cc_final: 0.6972 (m-10) REVERT: K 22 SER cc_start: 0.9111 (m) cc_final: 0.8885 (t) REVERT: K 58 LEU cc_start: 0.7898 (tp) cc_final: 0.7639 (tp) REVERT: K 60 ASP cc_start: 0.6306 (t0) cc_final: 0.5118 (t0) REVERT: K 92 ASP cc_start: 0.8340 (t0) cc_final: 0.8104 (m-30) REVERT: L 34 GLN cc_start: 0.7034 (pp30) cc_final: 0.6797 (pp30) REVERT: L 58 LEU cc_start: 0.7707 (tp) cc_final: 0.7460 (tp) REVERT: L 60 ASP cc_start: 0.7037 (t0) cc_final: 0.6207 (t0) REVERT: L 92 ASP cc_start: 0.8116 (t0) cc_final: 0.7791 (m-30) outliers start: 22 outliers final: 9 residues processed: 909 average time/residue: 0.1534 time to fit residues: 212.3218 Evaluate side-chains 569 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 560 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0060 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN A 651 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN B 258 GLN C 651 ASN C 656 ASN F 651 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 ASN G 156 GLN G 170 GLN G 425 ASN H 78 GLN I 137 ASN I 156 GLN I 170 GLN I 302 ASN I 425 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109830 restraints weight = 40639.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113351 restraints weight = 23963.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115791 restraints weight = 16410.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117473 restraints weight = 12445.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118688 restraints weight = 10171.732| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20499 Z= 0.177 Angle : 1.104 16.410 28028 Z= 0.499 Chirality : 0.061 0.641 3391 Planarity : 0.006 0.059 3389 Dihedral : 15.593 88.623 4566 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.52 % Favored : 88.39 % Rotamer: Outliers : 0.29 % Allowed : 5.32 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.62 % 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: -4.32 (0.15), residues: 2343 helix: -2.51 (0.23), residues: 336 sheet: -1.76 (0.23), residues: 429 loop : -3.53 (0.13), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 617 TYR 0.032 0.002 TYR I 173 PHE 0.039 0.002 PHE K 31 TRP 0.033 0.002 TRP F 610 HIS 0.009 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00365 (20371) covalent geometry : angle 1.00610 (27674) SS BOND : bond 0.00355 ( 30) SS BOND : angle 1.88144 ( 60) hydrogen bonds : bond 0.05670 ( 451) hydrogen bonds : angle 7.58834 ( 1239) link_ALPHA1-3 : bond 0.01034 ( 3) link_ALPHA1-3 : angle 3.66470 ( 9) link_ALPHA1-6 : bond 0.00963 ( 2) link_ALPHA1-6 : angle 1.37125 ( 6) link_BETA1-4 : bond 0.01132 ( 42) link_BETA1-4 : angle 4.34640 ( 126) link_NAG-ASN : bond 0.01140 ( 51) link_NAG-ASN : angle 4.74655 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 756 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 PHE cc_start: 0.8787 (t80) cc_final: 0.8522 (t80) REVERT: A 523 LEU cc_start: 0.9411 (mt) cc_final: 0.9052 (mt) REVERT: A 543 ASN cc_start: 0.9036 (t0) cc_final: 0.8331 (t0) REVERT: A 661 LEU cc_start: 0.8659 (tp) cc_final: 0.8352 (tt) REVERT: B 97 LYS cc_start: 0.9044 (mmtp) cc_final: 0.8514 (mmmm) REVERT: B 106 GLU cc_start: 0.8760 (pt0) cc_final: 0.8512 (tm-30) REVERT: B 182 VAL cc_start: 0.8982 (t) cc_final: 0.8719 (p) REVERT: B 265 LEU cc_start: 0.9128 (mt) cc_final: 0.8810 (mm) REVERT: B 279 ASN cc_start: 0.8257 (t0) cc_final: 0.7816 (t0) REVERT: B 321 ASP cc_start: 0.8953 (m-30) cc_final: 0.8725 (m-30) REVERT: B 474 ASP cc_start: 0.8645 (t70) cc_final: 0.8093 (t0) REVERT: B 485 LYS cc_start: 0.8661 (ptpt) cc_final: 0.8261 (ptpt) REVERT: B 492 GLU cc_start: 0.8766 (tp30) cc_final: 0.8282 (tm-30) REVERT: C 588 ARG cc_start: 0.8680 (ttt90) cc_final: 0.7951 (ttt180) REVERT: C 607 ASN cc_start: 0.8217 (t0) cc_final: 0.7874 (t0) REVERT: C 658 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8074 (tp-100) REVERT: D 48 TRP cc_start: 0.8829 (t60) cc_final: 0.8216 (t60) REVERT: D 57 ASN cc_start: 0.7591 (t0) cc_final: 0.7377 (t0) REVERT: D 58 THR cc_start: 0.8868 (p) cc_final: 0.8568 (m) REVERT: D 59 TYR cc_start: 0.7687 (m-80) cc_final: 0.7267 (m-10) REVERT: D 61 ASN cc_start: 0.7907 (t0) cc_final: 0.7691 (t0) REVERT: D 79 PHE cc_start: 0.8711 (p90) cc_final: 0.8463 (p90) REVERT: D 100 ASN cc_start: 0.8361 (p0) cc_final: 0.8125 (p0) REVERT: E 49 TYR cc_start: 0.7370 (t80) cc_final: 0.6987 (t80) REVERT: E 54 ARG cc_start: 0.8327 (mmm-85) cc_final: 0.7944 (mmp80) REVERT: E 60 ASP cc_start: 0.7757 (t0) cc_final: 0.6529 (t0) REVERT: E 92 ASP cc_start: 0.8988 (t0) cc_final: 0.8692 (m-30) REVERT: E 104 LEU cc_start: 0.8503 (pt) cc_final: 0.8265 (pp) REVERT: F 522 PHE cc_start: 0.8538 (t80) cc_final: 0.7943 (t80) REVERT: F 523 LEU cc_start: 0.9386 (mt) cc_final: 0.9153 (mt) REVERT: F 543 ASN cc_start: 0.8805 (t0) cc_final: 0.8167 (t0) REVERT: G 82 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8097 (mp10) REVERT: G 94 ASN cc_start: 0.8571 (t0) cc_final: 0.7963 (t0) REVERT: G 125 LEU cc_start: 0.9344 (mm) cc_final: 0.9130 (tt) REVERT: G 156 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: G 193 LEU cc_start: 0.7758 (pt) cc_final: 0.7425 (pp) REVERT: G 203 GLN cc_start: 0.8756 (pp30) cc_final: 0.8368 (pp30) REVERT: G 226 LEU cc_start: 0.8417 (pp) cc_final: 0.8080 (pp) REVERT: G 269 GLU cc_start: 0.8827 (tp30) cc_final: 0.8623 (tp30) REVERT: G 270 VAL cc_start: 0.9549 (t) cc_final: 0.9224 (t) REVERT: G 325 ASP cc_start: 0.8996 (p0) cc_final: 0.8770 (p0) REVERT: G 328 MET cc_start: 0.7524 (ptm) cc_final: 0.7189 (pmm) REVERT: G 368 ASP cc_start: 0.8392 (p0) cc_final: 0.8051 (t70) REVERT: G 369 LEU cc_start: 0.8667 (pp) cc_final: 0.8361 (mm) REVERT: G 425 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7570 (p0) REVERT: G 449 ILE cc_start: 0.6865 (mm) cc_final: 0.6623 (mm) REVERT: H 79 PHE cc_start: 0.8925 (p90) cc_final: 0.8668 (p90) REVERT: H 91 TYR cc_start: 0.8450 (m-10) cc_final: 0.7817 (m-10) REVERT: I 50 THR cc_start: 0.9593 (p) cc_final: 0.9316 (p) REVERT: I 53 PHE cc_start: 0.8595 (p90) cc_final: 0.8332 (p90) REVERT: I 87 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7757 (tm-30) REVERT: I 97 LYS cc_start: 0.9180 (mmtp) cc_final: 0.8675 (mmmm) REVERT: I 114 GLN cc_start: 0.9254 (tm-30) cc_final: 0.8944 (tm-30) REVERT: I 156 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: I 269 GLU cc_start: 0.9265 (tp30) cc_final: 0.8734 (tp30) REVERT: I 368 ASP cc_start: 0.8593 (t70) cc_final: 0.8252 (t70) REVERT: I 370 GLU cc_start: 0.8251 (mp0) cc_final: 0.7993 (mp0) REVERT: I 425 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7666 (p0) REVERT: I 426 MET cc_start: 0.7414 (ptt) cc_final: 0.7025 (ptm) REVERT: I 427 TRP cc_start: 0.8723 (m100) cc_final: 0.8035 (m100) REVERT: I 434 MET cc_start: 0.8752 (ttm) cc_final: 0.8432 (ttm) REVERT: I 478 ASN cc_start: 0.8285 (m110) cc_final: 0.7526 (m110) REVERT: I 499 THR cc_start: 0.8866 (t) cc_final: 0.8641 (t) REVERT: J 13 LYS cc_start: 0.7219 (mtmt) cc_final: 0.6890 (mtmt) REVERT: J 57 ASN cc_start: 0.7436 (t0) cc_final: 0.7210 (t0) REVERT: K 60 ASP cc_start: 0.7917 (t0) cc_final: 0.7004 (t0) REVERT: K 92 ASP cc_start: 0.9023 (t0) cc_final: 0.8669 (m-30) REVERT: L 49 TYR cc_start: 0.6879 (t80) cc_final: 0.6540 (t80) REVERT: L 60 ASP cc_start: 0.7849 (t0) cc_final: 0.7307 (t0) REVERT: L 92 ASP cc_start: 0.8884 (t0) cc_final: 0.8544 (m-30) outliers start: 6 outliers final: 0 residues processed: 758 average time/residue: 0.1411 time to fit residues: 167.5929 Evaluate side-chains 554 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 550 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 96 optimal weight: 0.7980 chunk 230 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 176 optimal weight: 0.0020 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN A 652 GLN B 156 GLN G 156 GLN H 78 GLN I 103 GLN I 137 ASN I 156 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109664 restraints weight = 40138.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.113110 restraints weight = 23537.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115470 restraints weight = 16068.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117130 restraints weight = 12196.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118313 restraints weight = 9940.162| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20499 Z= 0.157 Angle : 1.022 16.756 28028 Z= 0.460 Chirality : 0.058 0.563 3391 Planarity : 0.005 0.058 3389 Dihedral : 13.420 89.320 4566 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.55 % Favored : 87.37 % Rotamer: Outliers : 0.29 % Allowed : 4.98 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.95 (0.15), residues: 2343 helix: -2.03 (0.25), residues: 339 sheet: -1.30 (0.22), residues: 489 loop : -3.47 (0.14), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 54 TYR 0.035 0.002 TYR H 92 PHE 0.020 0.001 PHE I 320 TRP 0.058 0.002 TRP A 596 HIS 0.006 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00326 (20371) covalent geometry : angle 0.93228 (27674) SS BOND : bond 0.00884 ( 30) SS BOND : angle 1.47400 ( 60) hydrogen bonds : bond 0.04513 ( 451) hydrogen bonds : angle 6.92489 ( 1239) link_ALPHA1-3 : bond 0.01095 ( 3) link_ALPHA1-3 : angle 3.23571 ( 9) link_ALPHA1-6 : bond 0.00988 ( 2) link_ALPHA1-6 : angle 1.14496 ( 6) link_BETA1-4 : bond 0.01100 ( 42) link_BETA1-4 : angle 4.15468 ( 126) link_NAG-ASN : bond 0.00811 ( 51) link_NAG-ASN : angle 4.30776 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 699 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 PHE cc_start: 0.8859 (t80) cc_final: 0.8511 (t80) REVERT: A 523 LEU cc_start: 0.9408 (mt) cc_final: 0.8969 (mt) REVERT: A 543 ASN cc_start: 0.9148 (t0) cc_final: 0.8462 (t0) REVERT: A 588 ARG cc_start: 0.8810 (ttt90) cc_final: 0.7819 (ttt180) REVERT: A 630 GLN cc_start: 0.8833 (mp10) cc_final: 0.8573 (mp10) REVERT: B 97 LYS cc_start: 0.9045 (mmtp) cc_final: 0.8568 (mmmm) REVERT: B 106 GLU cc_start: 0.8646 (pt0) cc_final: 0.8279 (tm-30) REVERT: B 265 LEU cc_start: 0.9114 (mt) cc_final: 0.8826 (mm) REVERT: B 270 VAL cc_start: 0.9604 (t) cc_final: 0.9384 (p) REVERT: B 279 ASN cc_start: 0.8269 (t0) cc_final: 0.7823 (t0) REVERT: B 474 ASP cc_start: 0.8615 (t70) cc_final: 0.8051 (t0) REVERT: B 485 LYS cc_start: 0.8691 (ptpt) cc_final: 0.8286 (ptpt) REVERT: B 492 GLU cc_start: 0.8703 (tp30) cc_final: 0.8340 (tt0) REVERT: C 543 ASN cc_start: 0.9253 (t0) cc_final: 0.8815 (t0) REVERT: C 588 ARG cc_start: 0.8875 (ttt90) cc_final: 0.8511 (tpt-90) REVERT: C 607 ASN cc_start: 0.8261 (t0) cc_final: 0.7837 (t0) REVERT: C 630 GLN cc_start: 0.8878 (mp10) cc_final: 0.8586 (mp10) REVERT: C 658 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8138 (tp40) REVERT: D 48 TRP cc_start: 0.8751 (t60) cc_final: 0.8207 (t60) REVERT: D 52 ILE cc_start: 0.7082 (tp) cc_final: 0.6848 (tp) REVERT: D 57 ASN cc_start: 0.7803 (t0) cc_final: 0.7529 (t0) REVERT: D 58 THR cc_start: 0.8849 (p) cc_final: 0.8613 (m) REVERT: D 61 ASN cc_start: 0.8163 (t0) cc_final: 0.7802 (t0) REVERT: D 100 ASN cc_start: 0.8210 (p0) cc_final: 0.7997 (p0) REVERT: E 31 PHE cc_start: 0.6471 (t80) cc_final: 0.5786 (t80) REVERT: E 92 ASP cc_start: 0.8970 (t0) cc_final: 0.8657 (m-30) REVERT: E 104 LEU cc_start: 0.8302 (pt) cc_final: 0.7994 (pp) REVERT: F 522 PHE cc_start: 0.8760 (t80) cc_final: 0.8459 (t80) REVERT: F 543 ASN cc_start: 0.8885 (t0) cc_final: 0.8236 (t0) REVERT: F 638 TYR cc_start: 0.8234 (m-10) cc_final: 0.7914 (m-10) REVERT: G 82 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8142 (mp10) REVERT: G 92 GLU cc_start: 0.7499 (pp20) cc_final: 0.7031 (pp20) REVERT: G 95 MET cc_start: 0.9219 (ptm) cc_final: 0.8597 (ptm) REVERT: G 112 TRP cc_start: 0.8930 (t-100) cc_final: 0.8713 (t-100) REVERT: G 117 LYS cc_start: 0.9226 (tmtt) cc_final: 0.9010 (ttmt) REVERT: G 156 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: G 164 GLU cc_start: 0.9107 (pp20) cc_final: 0.8893 (pp20) REVERT: G 211 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8075 (tm-30) REVERT: G 225 ILE cc_start: 0.9020 (mm) cc_final: 0.8788 (mm) REVERT: G 226 LEU cc_start: 0.8553 (pp) cc_final: 0.8192 (pp) REVERT: G 477 ASP cc_start: 0.9316 (m-30) cc_final: 0.9105 (m-30) REVERT: H 67 ARG cc_start: 0.7941 (mmm160) cc_final: 0.7220 (mmm160) REVERT: H 79 PHE cc_start: 0.8770 (p90) cc_final: 0.8543 (p90) REVERT: H 91 TYR cc_start: 0.8597 (m-10) cc_final: 0.8243 (m-10) REVERT: I 50 THR cc_start: 0.9482 (p) cc_final: 0.9196 (p) REVERT: I 53 PHE cc_start: 0.8619 (p90) cc_final: 0.8387 (p90) REVERT: I 87 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7746 (tm-30) REVERT: I 92 GLU cc_start: 0.7677 (pp20) cc_final: 0.6891 (pp20) REVERT: I 97 LYS cc_start: 0.8821 (mmtp) cc_final: 0.8470 (mmmm) REVERT: I 106 GLU cc_start: 0.8443 (tt0) cc_final: 0.8021 (tm-30) REVERT: I 114 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8969 (tm-30) REVERT: I 156 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: I 180 ASP cc_start: 0.8073 (m-30) cc_final: 0.7779 (m-30) REVERT: I 211 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8329 (tm-30) REVERT: I 269 GLU cc_start: 0.9270 (tp30) cc_final: 0.8883 (tp30) REVERT: I 328 MET cc_start: 0.7654 (ptm) cc_final: 0.7303 (ptm) REVERT: I 340 GLU cc_start: 0.9122 (tt0) cc_final: 0.8674 (tp30) REVERT: I 421 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8806 (mtmt) REVERT: I 423 ILE cc_start: 0.8979 (pt) cc_final: 0.8761 (pt) REVERT: I 434 MET cc_start: 0.8795 (ttm) cc_final: 0.8236 (ttm) REVERT: I 485 LYS cc_start: 0.8716 (ptpt) cc_final: 0.8471 (ptpt) REVERT: I 499 THR cc_start: 0.8815 (t) cc_final: 0.8597 (t) REVERT: J 13 LYS cc_start: 0.7369 (mtmt) cc_final: 0.6966 (mtmt) REVERT: K 92 ASP cc_start: 0.8981 (t0) cc_final: 0.8574 (m-30) REVERT: L 22 SER cc_start: 0.8747 (t) cc_final: 0.8525 (m) REVERT: L 39 LEU cc_start: 0.5712 (tp) cc_final: 0.5478 (tp) REVERT: L 85 ASP cc_start: 0.7436 (m-30) cc_final: 0.7218 (m-30) outliers start: 6 outliers final: 1 residues processed: 701 average time/residue: 0.1395 time to fit residues: 153.4561 Evaluate side-chains 546 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 543 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 97 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 80 optimal weight: 0.0470 chunk 59 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 218 optimal weight: 0.2980 chunk 199 optimal weight: 0.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN G 99 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109632 restraints weight = 39967.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113065 restraints weight = 23476.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115463 restraints weight = 16056.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117153 restraints weight = 12160.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118326 restraints weight = 9895.101| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20499 Z= 0.147 Angle : 0.975 14.007 28028 Z= 0.438 Chirality : 0.056 0.503 3391 Planarity : 0.005 0.064 3389 Dihedral : 12.271 88.905 4566 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.99 % Favored : 87.92 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.80 (0.16), residues: 2343 helix: -1.82 (0.25), residues: 330 sheet: -1.41 (0.22), residues: 510 loop : -3.31 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 429 TYR 0.042 0.002 TYR I 217 PHE 0.020 0.001 PHE I 320 TRP 0.048 0.002 TRP G 96 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00314 (20371) covalent geometry : angle 0.89229 (27674) SS BOND : bond 0.00542 ( 30) SS BOND : angle 1.73186 ( 60) hydrogen bonds : bond 0.03941 ( 451) hydrogen bonds : angle 6.40274 ( 1239) link_ALPHA1-3 : bond 0.00866 ( 3) link_ALPHA1-3 : angle 3.32377 ( 9) link_ALPHA1-6 : bond 0.01141 ( 2) link_ALPHA1-6 : angle 1.19090 ( 6) link_BETA1-4 : bond 0.00986 ( 42) link_BETA1-4 : angle 3.90446 ( 126) link_NAG-ASN : bond 0.00882 ( 51) link_NAG-ASN : angle 3.96524 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 PHE cc_start: 0.8864 (t80) cc_final: 0.8489 (t80) REVERT: A 523 LEU cc_start: 0.9298 (mt) cc_final: 0.8869 (mt) REVERT: A 530 MET cc_start: 0.8723 (mmm) cc_final: 0.8522 (mmm) REVERT: A 535 MET cc_start: 0.8907 (mmt) cc_final: 0.8675 (mmp) REVERT: A 543 ASN cc_start: 0.9167 (t0) cc_final: 0.8408 (t0) REVERT: A 588 ARG cc_start: 0.9041 (ttt90) cc_final: 0.8019 (ttt180) REVERT: A 630 GLN cc_start: 0.8868 (mp10) cc_final: 0.8616 (mp10) REVERT: B 92 GLU cc_start: 0.5573 (pp20) cc_final: 0.5111 (pp20) REVERT: B 96 TRP cc_start: 0.9278 (m100) cc_final: 0.8640 (m100) REVERT: B 106 GLU cc_start: 0.8416 (pt0) cc_final: 0.8212 (tm-30) REVERT: B 166 ARG cc_start: 0.7314 (tmm-80) cc_final: 0.7057 (ptm-80) REVERT: B 279 ASN cc_start: 0.8400 (t0) cc_final: 0.8064 (t0) REVERT: B 474 ASP cc_start: 0.8613 (t70) cc_final: 0.8134 (t0) REVERT: B 485 LYS cc_start: 0.8758 (ptpt) cc_final: 0.8426 (ptpt) REVERT: B 492 GLU cc_start: 0.8577 (tp30) cc_final: 0.8259 (tt0) REVERT: C 522 PHE cc_start: 0.9262 (t80) cc_final: 0.9050 (t80) REVERT: C 543 ASN cc_start: 0.9282 (t0) cc_final: 0.8848 (t0) REVERT: C 588 ARG cc_start: 0.9032 (ttt90) cc_final: 0.8719 (tpt-90) REVERT: C 607 ASN cc_start: 0.8105 (t0) cc_final: 0.7702 (t0) REVERT: C 624 ASP cc_start: 0.7811 (m-30) cc_final: 0.7570 (m-30) REVERT: C 658 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8078 (tp40) REVERT: D 48 TRP cc_start: 0.8729 (t60) cc_final: 0.8292 (t60) REVERT: D 52 ILE cc_start: 0.6622 (tp) cc_final: 0.6355 (tp) REVERT: D 58 THR cc_start: 0.8981 (p) cc_final: 0.8660 (m) REVERT: D 61 ASN cc_start: 0.8391 (t0) cc_final: 0.7912 (t0) REVERT: D 78 GLN cc_start: 0.7246 (mp-120) cc_final: 0.6739 (mp10) REVERT: D 100 ASN cc_start: 0.8364 (p0) cc_final: 0.8032 (p0) REVERT: E 31 PHE cc_start: 0.6696 (t80) cc_final: 0.5987 (t80) REVERT: E 92 ASP cc_start: 0.8945 (t0) cc_final: 0.8521 (m-30) REVERT: E 104 LEU cc_start: 0.8194 (pt) cc_final: 0.7872 (pp) REVERT: F 522 PHE cc_start: 0.8816 (t80) cc_final: 0.8562 (t80) REVERT: F 543 ASN cc_start: 0.8945 (t0) cc_final: 0.8300 (t0) REVERT: F 630 GLN cc_start: 0.8772 (mp10) cc_final: 0.8526 (mp10) REVERT: F 638 TYR cc_start: 0.8219 (m-10) cc_final: 0.7888 (m-10) REVERT: G 49 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7536 (tm-30) REVERT: G 82 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8190 (mp10) REVERT: G 92 GLU cc_start: 0.7570 (pp20) cc_final: 0.7241 (pp20) REVERT: G 113 ASP cc_start: 0.9298 (t0) cc_final: 0.9087 (t70) REVERT: G 164 GLU cc_start: 0.9021 (pp20) cc_final: 0.8809 (pp20) REVERT: G 195 ASN cc_start: 0.7436 (t0) cc_final: 0.7034 (t0) REVERT: G 478 ASN cc_start: 0.7617 (m110) cc_final: 0.7337 (m110) REVERT: G 499 THR cc_start: 0.8432 (t) cc_final: 0.8216 (t) REVERT: H 57 ASN cc_start: 0.7928 (t0) cc_final: 0.7688 (t0) REVERT: H 67 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7398 (mmm160) REVERT: H 79 PHE cc_start: 0.8165 (p90) cc_final: 0.7846 (p90) REVERT: H 91 TYR cc_start: 0.8486 (m-10) cc_final: 0.7974 (m-10) REVERT: I 50 THR cc_start: 0.9406 (p) cc_final: 0.9124 (p) REVERT: I 53 PHE cc_start: 0.8781 (p90) cc_final: 0.8530 (p90) REVERT: I 57 ASP cc_start: 0.7167 (p0) cc_final: 0.6938 (p0) REVERT: I 110 SER cc_start: 0.9478 (m) cc_final: 0.9227 (t) REVERT: I 114 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8898 (tm-30) REVERT: I 307 ILE cc_start: 0.8873 (mm) cc_final: 0.8580 (tp) REVERT: I 340 GLU cc_start: 0.9091 (tt0) cc_final: 0.8597 (tp30) REVERT: I 421 LYS cc_start: 0.9141 (ttmt) cc_final: 0.8818 (mtmt) REVERT: I 426 MET cc_start: 0.7212 (ptt) cc_final: 0.6910 (ptt) REVERT: I 434 MET cc_start: 0.8779 (ttm) cc_final: 0.8234 (ttm) REVERT: J 13 LYS cc_start: 0.7391 (mtmt) cc_final: 0.7041 (mtmt) REVERT: J 40 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8066 (tm-30) REVERT: J 57 ASN cc_start: 0.7710 (t0) cc_final: 0.7438 (t0) REVERT: J 79 PHE cc_start: 0.8703 (p90) cc_final: 0.8453 (p90) REVERT: K 31 PHE cc_start: 0.7415 (t80) cc_final: 0.6289 (t80) REVERT: K 60 ASP cc_start: 0.8451 (t0) cc_final: 0.7816 (t0) REVERT: L 34 GLN cc_start: 0.6811 (pp30) cc_final: 0.6377 (pp30) REVERT: L 39 LEU cc_start: 0.5993 (tp) cc_final: 0.5779 (tp) outliers start: 0 outliers final: 0 residues processed: 682 average time/residue: 0.1362 time to fit residues: 145.9703 Evaluate side-chains 536 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 0.0040 chunk 28 optimal weight: 6.9990 chunk 191 optimal weight: 0.0270 chunk 155 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 146 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.8454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 ASN I 203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108510 restraints weight = 40065.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111806 restraints weight = 23952.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114118 restraints weight = 16602.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115690 restraints weight = 12694.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116842 restraints weight = 10436.162| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20499 Z= 0.141 Angle : 0.927 13.299 28028 Z= 0.416 Chirality : 0.054 0.466 3391 Planarity : 0.004 0.052 3389 Dihedral : 11.585 87.835 4566 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.91 % Favored : 88.01 % Rotamer: Outliers : 0.14 % Allowed : 3.35 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.67 (0.16), residues: 2343 helix: -1.63 (0.25), residues: 351 sheet: -1.38 (0.22), residues: 516 loop : -3.25 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 617 TYR 0.046 0.002 TYR B 173 PHE 0.020 0.001 PHE I 320 TRP 0.020 0.002 TRP H 34 HIS 0.009 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00308 (20371) covalent geometry : angle 0.84911 (27674) SS BOND : bond 0.00940 ( 30) SS BOND : angle 1.71642 ( 60) hydrogen bonds : bond 0.03646 ( 451) hydrogen bonds : angle 6.13551 ( 1239) link_ALPHA1-3 : bond 0.00897 ( 3) link_ALPHA1-3 : angle 3.14052 ( 9) link_ALPHA1-6 : bond 0.01251 ( 2) link_ALPHA1-6 : angle 1.21193 ( 6) link_BETA1-4 : bond 0.00894 ( 42) link_BETA1-4 : angle 3.66022 ( 126) link_NAG-ASN : bond 0.00668 ( 51) link_NAG-ASN : angle 3.74723 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 661 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 PHE cc_start: 0.8850 (t80) cc_final: 0.8420 (t80) REVERT: A 523 LEU cc_start: 0.9350 (mt) cc_final: 0.8885 (mt) REVERT: A 535 MET cc_start: 0.8741 (mmt) cc_final: 0.8506 (mmp) REVERT: A 543 ASN cc_start: 0.9216 (t0) cc_final: 0.8480 (t0) REVERT: A 575 GLN cc_start: 0.8031 (mm110) cc_final: 0.7825 (mm110) REVERT: A 584 GLU cc_start: 0.8776 (tt0) cc_final: 0.8453 (tt0) REVERT: A 588 ARG cc_start: 0.8991 (ttt90) cc_final: 0.8522 (tpt-90) REVERT: A 607 ASN cc_start: 0.8093 (t0) cc_final: 0.7891 (t0) REVERT: A 620 SER cc_start: 0.8607 (p) cc_final: 0.8012 (p) REVERT: A 630 GLN cc_start: 0.8915 (mp10) cc_final: 0.8257 (mp10) REVERT: B 96 TRP cc_start: 0.9339 (m100) cc_final: 0.8673 (m100) REVERT: B 106 GLU cc_start: 0.8575 (pt0) cc_final: 0.8293 (tm-30) REVERT: B 167 ASP cc_start: 0.9531 (p0) cc_final: 0.9310 (p0) REVERT: B 279 ASN cc_start: 0.8661 (t0) cc_final: 0.8223 (t0) REVERT: B 328 MET cc_start: 0.6563 (pmm) cc_final: 0.6267 (pmm) REVERT: B 368 ASP cc_start: 0.7767 (t70) cc_final: 0.7486 (t70) REVERT: B 474 ASP cc_start: 0.8619 (t70) cc_final: 0.8063 (t0) REVERT: B 485 LYS cc_start: 0.8678 (ptpt) cc_final: 0.8324 (ptpt) REVERT: B 492 GLU cc_start: 0.8689 (tp30) cc_final: 0.8256 (tt0) REVERT: C 543 ASN cc_start: 0.9213 (t0) cc_final: 0.8769 (t0) REVERT: C 588 ARG cc_start: 0.9149 (ttt90) cc_final: 0.8884 (tpt-90) REVERT: C 607 ASN cc_start: 0.8197 (t0) cc_final: 0.7850 (t0) REVERT: C 658 GLN cc_start: 0.8526 (tp-100) cc_final: 0.7836 (tp40) REVERT: D 47 GLU cc_start: 0.7967 (tp30) cc_final: 0.7766 (tp30) REVERT: D 48 TRP cc_start: 0.8713 (t60) cc_final: 0.8427 (t60) REVERT: D 52 ILE cc_start: 0.6715 (tp) cc_final: 0.6472 (tp) REVERT: D 58 THR cc_start: 0.8748 (p) cc_final: 0.8497 (m) REVERT: D 61 ASN cc_start: 0.8249 (t0) cc_final: 0.7910 (t0) REVERT: D 67 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7753 (mmm160) REVERT: E 31 PHE cc_start: 0.6440 (t80) cc_final: 0.5742 (t80) REVERT: E 92 ASP cc_start: 0.8954 (t0) cc_final: 0.8472 (m-30) REVERT: E 104 LEU cc_start: 0.8102 (pt) cc_final: 0.7782 (pp) REVERT: F 522 PHE cc_start: 0.8888 (t80) cc_final: 0.8466 (t80) REVERT: F 523 LEU cc_start: 0.9213 (mt) cc_final: 0.8856 (mt) REVERT: F 543 ASN cc_start: 0.8963 (t0) cc_final: 0.8267 (t0) REVERT: F 607 ASN cc_start: 0.7908 (t0) cc_final: 0.7535 (t0) REVERT: F 630 GLN cc_start: 0.8728 (mp10) cc_final: 0.8470 (mp10) REVERT: F 638 TYR cc_start: 0.8348 (m-10) cc_final: 0.8016 (m-10) REVERT: G 82 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8179 (mp10) REVERT: G 92 GLU cc_start: 0.7532 (pp20) cc_final: 0.7225 (pp20) REVERT: G 98 ASN cc_start: 0.8711 (t0) cc_final: 0.8450 (t0) REVERT: G 99 ASN cc_start: 0.8932 (p0) cc_final: 0.8644 (p0) REVERT: G 113 ASP cc_start: 0.9387 (t0) cc_final: 0.9036 (t70) REVERT: G 156 GLN cc_start: 0.7550 (pp30) cc_final: 0.7081 (pm20) REVERT: G 164 GLU cc_start: 0.9105 (pp20) cc_final: 0.8814 (pp20) REVERT: G 195 ASN cc_start: 0.7462 (t0) cc_final: 0.7047 (t0) REVERT: G 211 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8104 (tm-30) REVERT: G 325 ASP cc_start: 0.9020 (p0) cc_final: 0.8813 (p0) REVERT: G 350 ARG cc_start: 0.8232 (tpt-90) cc_final: 0.7926 (tpt-90) REVERT: G 363 GLN cc_start: 0.8925 (pp30) cc_final: 0.8690 (pp30) REVERT: G 368 ASP cc_start: 0.8333 (t70) cc_final: 0.8120 (t70) REVERT: G 477 ASP cc_start: 0.9353 (m-30) cc_final: 0.9114 (m-30) REVERT: G 499 THR cc_start: 0.8384 (t) cc_final: 0.8127 (t) REVERT: H 57 ASN cc_start: 0.7756 (t0) cc_final: 0.7555 (t0) REVERT: H 67 ARG cc_start: 0.8124 (mmm160) cc_final: 0.7359 (mmm160) REVERT: H 91 TYR cc_start: 0.8660 (m-10) cc_final: 0.8124 (m-10) REVERT: I 50 THR cc_start: 0.9455 (p) cc_final: 0.9164 (p) REVERT: I 53 PHE cc_start: 0.8695 (p90) cc_final: 0.8464 (p90) REVERT: I 110 SER cc_start: 0.9383 (m) cc_final: 0.9130 (t) REVERT: I 114 GLN cc_start: 0.9359 (tm-30) cc_final: 0.9124 (tm-30) REVERT: I 150 MET cc_start: 0.8743 (mpp) cc_final: 0.7744 (mpp) REVERT: I 211 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8284 (tm-30) REVERT: I 307 ILE cc_start: 0.8953 (mm) cc_final: 0.8652 (tp) REVERT: I 340 GLU cc_start: 0.9117 (tt0) cc_final: 0.8679 (tp30) REVERT: I 426 MET cc_start: 0.7515 (ptt) cc_final: 0.7133 (ptt) REVERT: I 434 MET cc_start: 0.8898 (ttm) cc_final: 0.8570 (ttm) REVERT: J 47 GLU cc_start: 0.7909 (tp30) cc_final: 0.7680 (tp30) REVERT: J 57 ASN cc_start: 0.7675 (t0) cc_final: 0.7430 (t0) REVERT: K 60 ASP cc_start: 0.8439 (t0) cc_final: 0.7922 (t0) REVERT: L 60 ASP cc_start: 0.8023 (t0) cc_final: 0.7619 (t0) outliers start: 3 outliers final: 0 residues processed: 663 average time/residue: 0.1362 time to fit residues: 141.7742 Evaluate side-chains 516 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 187 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 220 optimal weight: 0.2980 chunk 195 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 195 ASN E 6 GLN G 156 GLN H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107857 restraints weight = 39614.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111169 restraints weight = 23390.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113479 restraints weight = 16062.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115087 restraints weight = 12176.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116240 restraints weight = 9940.071| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20499 Z= 0.143 Angle : 0.922 13.517 28028 Z= 0.415 Chirality : 0.053 0.460 3391 Planarity : 0.004 0.048 3389 Dihedral : 11.108 85.106 4566 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.99 % Favored : 87.92 % Rotamer: Outliers : 0.14 % Allowed : 1.92 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.58 (0.16), residues: 2343 helix: -1.31 (0.26), residues: 351 sheet: -1.32 (0.22), residues: 522 loop : -3.26 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.038 0.002 TYR B 173 PHE 0.020 0.001 PHE I 320 TRP 0.029 0.002 TRP B 427 HIS 0.008 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00317 (20371) covalent geometry : angle 0.84827 (27674) SS BOND : bond 0.00461 ( 30) SS BOND : angle 1.90511 ( 60) hydrogen bonds : bond 0.03564 ( 451) hydrogen bonds : angle 6.03260 ( 1239) link_ALPHA1-3 : bond 0.00747 ( 3) link_ALPHA1-3 : angle 3.06864 ( 9) link_ALPHA1-6 : bond 0.01325 ( 2) link_ALPHA1-6 : angle 1.36540 ( 6) link_BETA1-4 : bond 0.00859 ( 42) link_BETA1-4 : angle 3.47773 ( 126) link_NAG-ASN : bond 0.00582 ( 51) link_NAG-ASN : angle 3.66070 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 651 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 PHE cc_start: 0.8860 (t80) cc_final: 0.8522 (t80) REVERT: A 523 LEU cc_start: 0.9363 (mt) cc_final: 0.8915 (mt) REVERT: A 535 MET cc_start: 0.8783 (mmt) cc_final: 0.8553 (mmp) REVERT: A 543 ASN cc_start: 0.9257 (t0) cc_final: 0.8517 (t0) REVERT: A 575 GLN cc_start: 0.7805 (mm110) cc_final: 0.7577 (mm110) REVERT: A 584 GLU cc_start: 0.8989 (tt0) cc_final: 0.8758 (tt0) REVERT: A 620 SER cc_start: 0.8692 (p) cc_final: 0.8106 (p) REVERT: A 630 GLN cc_start: 0.8756 (mp10) cc_final: 0.8486 (mp10) REVERT: A 647 GLU cc_start: 0.7512 (tp30) cc_final: 0.7036 (tp30) REVERT: B 92 GLU cc_start: 0.5596 (pp20) cc_final: 0.5099 (pp20) REVERT: B 96 TRP cc_start: 0.9368 (m100) cc_final: 0.8771 (m100) REVERT: B 150 MET cc_start: 0.8870 (mmp) cc_final: 0.8652 (mpp) REVERT: B 167 ASP cc_start: 0.9458 (p0) cc_final: 0.9250 (p0) REVERT: B 195 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7633 (t160) REVERT: B 217 TYR cc_start: 0.7152 (m-10) cc_final: 0.6939 (m-10) REVERT: B 279 ASN cc_start: 0.8772 (t0) cc_final: 0.8435 (t0) REVERT: B 368 ASP cc_start: 0.7887 (t70) cc_final: 0.7660 (t70) REVERT: B 426 MET cc_start: 0.9040 (ppp) cc_final: 0.8801 (tmm) REVERT: B 474 ASP cc_start: 0.8672 (t70) cc_final: 0.8057 (t0) REVERT: B 485 LYS cc_start: 0.8786 (ptpt) cc_final: 0.8429 (ptpt) REVERT: B 492 GLU cc_start: 0.8683 (tp30) cc_final: 0.8222 (tt0) REVERT: C 538 THR cc_start: 0.8903 (p) cc_final: 0.8676 (p) REVERT: C 588 ARG cc_start: 0.9180 (ttt90) cc_final: 0.8936 (tpt-90) REVERT: C 607 ASN cc_start: 0.8220 (t0) cc_final: 0.7818 (t0) REVERT: C 658 GLN cc_start: 0.8573 (tp-100) cc_final: 0.7846 (tp40) REVERT: D 40 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8001 (tm-30) REVERT: D 52 ILE cc_start: 0.6997 (tp) cc_final: 0.6475 (tp) REVERT: D 58 THR cc_start: 0.8787 (p) cc_final: 0.8516 (m) REVERT: D 61 ASN cc_start: 0.8382 (t0) cc_final: 0.8032 (t0) REVERT: D 67 ARG cc_start: 0.8269 (mmm160) cc_final: 0.7648 (mmm160) REVERT: E 31 PHE cc_start: 0.6546 (t80) cc_final: 0.5808 (t80) REVERT: E 60 ASP cc_start: 0.7813 (t0) cc_final: 0.7406 (t0) REVERT: E 104 LEU cc_start: 0.8163 (pt) cc_final: 0.7921 (pp) REVERT: F 522 PHE cc_start: 0.8991 (t80) cc_final: 0.8589 (t80) REVERT: F 523 LEU cc_start: 0.9263 (mt) cc_final: 0.8947 (mt) REVERT: F 543 ASN cc_start: 0.9086 (t0) cc_final: 0.8485 (t0) REVERT: F 607 ASN cc_start: 0.7883 (t0) cc_final: 0.7465 (t0) REVERT: F 630 GLN cc_start: 0.8656 (mp10) cc_final: 0.8339 (mp10) REVERT: F 638 TYR cc_start: 0.8324 (m-10) cc_final: 0.7950 (m-10) REVERT: F 664 ASP cc_start: 0.6670 (p0) cc_final: 0.6455 (p0) REVERT: G 82 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8163 (mp10) REVERT: G 92 GLU cc_start: 0.7603 (pp20) cc_final: 0.7331 (pp20) REVERT: G 98 ASN cc_start: 0.8699 (t0) cc_final: 0.8398 (t0) REVERT: G 99 ASN cc_start: 0.9081 (p0) cc_final: 0.8775 (p0) REVERT: G 110 SER cc_start: 0.9496 (m) cc_final: 0.9235 (t) REVERT: G 113 ASP cc_start: 0.9410 (t0) cc_final: 0.9079 (t70) REVERT: G 156 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7153 (pm20) REVERT: G 164 GLU cc_start: 0.9122 (pp20) cc_final: 0.8833 (pp20) REVERT: G 170 GLN cc_start: 0.7173 (tt0) cc_final: 0.6599 (mt0) REVERT: G 171 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8096 (ttpp) REVERT: G 195 ASN cc_start: 0.7812 (t0) cc_final: 0.7409 (t0) REVERT: G 211 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8017 (tm-30) REVERT: G 325 ASP cc_start: 0.9045 (p0) cc_final: 0.8842 (p0) REVERT: G 350 ARG cc_start: 0.8317 (tpt-90) cc_final: 0.7956 (tpt-90) REVERT: G 363 GLN cc_start: 0.9075 (pp30) cc_final: 0.8732 (pp30) REVERT: G 368 ASP cc_start: 0.8015 (t70) cc_final: 0.7641 (t70) REVERT: G 475 MET cc_start: 0.8026 (tpp) cc_final: 0.7644 (tpp) REVERT: G 499 THR cc_start: 0.8390 (t) cc_final: 0.8110 (t) REVERT: H 40 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8146 (tm-30) REVERT: H 47 GLU cc_start: 0.7864 (tp30) cc_final: 0.7563 (tp30) REVERT: H 48 TRP cc_start: 0.9201 (t60) cc_final: 0.8196 (t60) REVERT: H 78 GLN cc_start: 0.7576 (mp10) cc_final: 0.7026 (mp10) REVERT: I 50 THR cc_start: 0.9437 (p) cc_final: 0.9140 (p) REVERT: I 53 PHE cc_start: 0.8638 (p90) cc_final: 0.8382 (p90) REVERT: I 110 SER cc_start: 0.9387 (m) cc_final: 0.9132 (t) REVERT: I 114 GLN cc_start: 0.9411 (tm-30) cc_final: 0.9162 (tm-30) REVERT: I 150 MET cc_start: 0.8696 (mpp) cc_final: 0.8178 (mpp) REVERT: I 195 ASN cc_start: 0.7906 (t0) cc_final: 0.7582 (t0) REVERT: I 211 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8228 (tm-30) REVERT: I 307 ILE cc_start: 0.8921 (mm) cc_final: 0.8619 (tp) REVERT: I 328 MET cc_start: 0.7697 (ptm) cc_final: 0.7367 (ptm) REVERT: I 340 GLU cc_start: 0.9173 (tt0) cc_final: 0.8692 (tp30) REVERT: I 434 MET cc_start: 0.8930 (ttm) cc_final: 0.8231 (ttm) REVERT: J 40 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8164 (tm-30) REVERT: J 61 ASN cc_start: 0.8267 (t0) cc_final: 0.7774 (t0) REVERT: K 60 ASP cc_start: 0.8533 (t0) cc_final: 0.8033 (t0) REVERT: L 60 ASP cc_start: 0.7973 (t0) cc_final: 0.7617 (t0) outliers start: 3 outliers final: 1 residues processed: 653 average time/residue: 0.1383 time to fit residues: 143.1573 Evaluate side-chains 512 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 509 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 198 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 52 optimal weight: 0.0020 chunk 2 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 51 ASN D 77 ASN D 78 GLN G 156 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.108064 restraints weight = 39547.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111404 restraints weight = 23434.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.113710 restraints weight = 16103.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115334 restraints weight = 12250.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116482 restraints weight = 10003.123| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20499 Z= 0.133 Angle : 0.909 12.284 28028 Z= 0.409 Chirality : 0.053 0.451 3391 Planarity : 0.004 0.048 3389 Dihedral : 10.730 84.219 4566 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.52 % Favored : 88.43 % Rotamer: Outliers : 0.05 % Allowed : 2.20 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.43 (0.16), residues: 2343 helix: -1.04 (0.27), residues: 333 sheet: -1.11 (0.23), residues: 510 loop : -3.21 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 95 TYR 0.031 0.001 TYR B 173 PHE 0.020 0.001 PHE I 320 TRP 0.038 0.002 TRP G 427 HIS 0.008 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00291 (20371) covalent geometry : angle 0.83689 (27674) SS BOND : bond 0.00417 ( 30) SS BOND : angle 2.02398 ( 60) hydrogen bonds : bond 0.03438 ( 451) hydrogen bonds : angle 5.89083 ( 1239) link_ALPHA1-3 : bond 0.00750 ( 3) link_ALPHA1-3 : angle 3.00559 ( 9) link_ALPHA1-6 : bond 0.01387 ( 2) link_ALPHA1-6 : angle 1.70456 ( 6) link_BETA1-4 : bond 0.00858 ( 42) link_BETA1-4 : angle 3.36205 ( 126) link_NAG-ASN : bond 0.00568 ( 51) link_NAG-ASN : angle 3.61329 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 656 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 PHE cc_start: 0.8930 (t80) cc_final: 0.8601 (t80) REVERT: A 523 LEU cc_start: 0.9318 (mt) cc_final: 0.8864 (mt) REVERT: A 535 MET cc_start: 0.8764 (mmt) cc_final: 0.8535 (mmp) REVERT: A 543 ASN cc_start: 0.9091 (t0) cc_final: 0.8293 (t0) REVERT: A 620 SER cc_start: 0.8601 (p) cc_final: 0.7992 (p) REVERT: A 622 ILE cc_start: 0.8788 (mm) cc_final: 0.8508 (mt) REVERT: A 630 GLN cc_start: 0.8868 (mp10) cc_final: 0.8547 (mp10) REVERT: A 651 ASN cc_start: 0.7434 (m110) cc_final: 0.7058 (m-40) REVERT: B 96 TRP cc_start: 0.9317 (m100) cc_final: 0.8826 (m100) REVERT: B 104 MET cc_start: 0.7903 (ttp) cc_final: 0.7570 (ttp) REVERT: B 106 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8055 (tm-30) REVERT: B 167 ASP cc_start: 0.9431 (p0) cc_final: 0.9219 (p0) REVERT: B 217 TYR cc_start: 0.7323 (m-10) cc_final: 0.7082 (m-10) REVERT: B 279 ASN cc_start: 0.8808 (t0) cc_final: 0.8524 (t0) REVERT: B 474 ASP cc_start: 0.8653 (t70) cc_final: 0.8024 (t0) REVERT: B 485 LYS cc_start: 0.8702 (ptpt) cc_final: 0.8376 (ptpt) REVERT: B 492 GLU cc_start: 0.8544 (tp30) cc_final: 0.8153 (tp30) REVERT: C 543 ASN cc_start: 0.9082 (t0) cc_final: 0.8629 (t0) REVERT: C 576 LEU cc_start: 0.8739 (mp) cc_final: 0.7950 (tt) REVERT: C 588 ARG cc_start: 0.9149 (ttt90) cc_final: 0.8890 (tpt-90) REVERT: C 607 ASN cc_start: 0.8222 (t0) cc_final: 0.7868 (t0) REVERT: C 628 TRP cc_start: 0.9197 (m100) cc_final: 0.8939 (m100) REVERT: C 658 GLN cc_start: 0.8547 (tp-100) cc_final: 0.7812 (tp40) REVERT: D 40 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8295 (tm-30) REVERT: D 52 ILE cc_start: 0.6906 (tp) cc_final: 0.6557 (tp) REVERT: D 61 ASN cc_start: 0.8381 (t0) cc_final: 0.8111 (t0) REVERT: D 67 ARG cc_start: 0.8124 (mmm160) cc_final: 0.7587 (mmm160) REVERT: D 70 ILE cc_start: 0.9256 (mp) cc_final: 0.8919 (mm) REVERT: E 31 PHE cc_start: 0.6666 (t80) cc_final: 0.5931 (t80) REVERT: E 60 ASP cc_start: 0.7901 (t0) cc_final: 0.7486 (t0) REVERT: E 104 LEU cc_start: 0.8102 (pt) cc_final: 0.7832 (pp) REVERT: F 522 PHE cc_start: 0.8988 (t80) cc_final: 0.8612 (t80) REVERT: F 523 LEU cc_start: 0.9163 (mt) cc_final: 0.8919 (mt) REVERT: F 530 MET cc_start: 0.8862 (mmm) cc_final: 0.8621 (mmt) REVERT: F 543 ASN cc_start: 0.9082 (t0) cc_final: 0.8476 (t0) REVERT: F 630 GLN cc_start: 0.8671 (mp10) cc_final: 0.8469 (mp10) REVERT: F 638 TYR cc_start: 0.8286 (m-10) cc_final: 0.7874 (m-10) REVERT: F 664 ASP cc_start: 0.6374 (p0) cc_final: 0.6073 (p0) REVERT: G 82 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8051 (mp10) REVERT: G 92 GLU cc_start: 0.7536 (pp20) cc_final: 0.7294 (pp20) REVERT: G 98 ASN cc_start: 0.8494 (t0) cc_final: 0.8218 (t0) REVERT: G 99 ASN cc_start: 0.9170 (p0) cc_final: 0.8843 (p0) REVERT: G 113 ASP cc_start: 0.9334 (t0) cc_final: 0.9009 (t70) REVERT: G 156 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: G 164 GLU cc_start: 0.9054 (pp20) cc_final: 0.8797 (pp20) REVERT: G 166 ARG cc_start: 0.8142 (tmm-80) cc_final: 0.7682 (ttp80) REVERT: G 171 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8201 (ttpp) REVERT: G 195 ASN cc_start: 0.7739 (t0) cc_final: 0.7205 (t0) REVERT: G 211 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7954 (tm-30) REVERT: G 350 ARG cc_start: 0.8279 (tpt-90) cc_final: 0.7946 (tpt-90) REVERT: G 368 ASP cc_start: 0.7838 (t70) cc_final: 0.7623 (t70) REVERT: H 40 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8270 (tm-30) REVERT: H 47 GLU cc_start: 0.8240 (tp30) cc_final: 0.7884 (tp30) REVERT: H 48 TRP cc_start: 0.9164 (t60) cc_final: 0.8522 (t60) REVERT: I 50 THR cc_start: 0.9435 (p) cc_final: 0.9086 (p) REVERT: I 53 PHE cc_start: 0.8765 (p90) cc_final: 0.8557 (p90) REVERT: I 110 SER cc_start: 0.9391 (m) cc_final: 0.9074 (t) REVERT: I 150 MET cc_start: 0.8627 (mpp) cc_final: 0.8108 (mpp) REVERT: I 195 ASN cc_start: 0.7720 (t0) cc_final: 0.7382 (t0) REVERT: I 211 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8239 (tm-30) REVERT: I 307 ILE cc_start: 0.8975 (mm) cc_final: 0.8664 (tp) REVERT: I 315 GLN cc_start: 0.8519 (mm-40) cc_final: 0.7817 (mp10) REVERT: I 319 TYR cc_start: 0.8562 (p90) cc_final: 0.8218 (p90) REVERT: I 328 MET cc_start: 0.7597 (ptm) cc_final: 0.7347 (ptm) REVERT: I 340 GLU cc_start: 0.9096 (tt0) cc_final: 0.8585 (tp30) REVERT: I 363 GLN cc_start: 0.8842 (pp30) cc_final: 0.8497 (pp30) REVERT: I 426 MET cc_start: 0.7381 (ptt) cc_final: 0.7114 (ptt) REVERT: I 477 ASP cc_start: 0.9237 (m-30) cc_final: 0.8900 (m-30) REVERT: J 20 LEU cc_start: 0.8962 (mp) cc_final: 0.8673 (mp) REVERT: J 40 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8230 (tm-30) REVERT: J 48 TRP cc_start: 0.9186 (t60) cc_final: 0.8636 (t60) REVERT: J 61 ASN cc_start: 0.8391 (t0) cc_final: 0.8016 (t0) REVERT: K 60 ASP cc_start: 0.8619 (t0) cc_final: 0.8124 (t0) REVERT: L 34 GLN cc_start: 0.6984 (pp30) cc_final: 0.6493 (pp30) REVERT: L 60 ASP cc_start: 0.8099 (t0) cc_final: 0.7771 (t0) outliers start: 1 outliers final: 0 residues processed: 656 average time/residue: 0.1308 time to fit residues: 135.8079 Evaluate side-chains 525 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 524 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 215 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN D 78 GLN G 137 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.102164 restraints weight = 40283.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105310 restraints weight = 23911.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107491 restraints weight = 16535.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109035 restraints weight = 12666.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110064 restraints weight = 10405.952| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20499 Z= 0.183 Angle : 0.949 16.403 28028 Z= 0.435 Chirality : 0.053 0.420 3391 Planarity : 0.005 0.047 3389 Dihedral : 10.724 80.689 4566 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.32 % Favored : 86.64 % Rotamer: Outliers : 0.10 % Allowed : 1.34 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.31 % 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: -3.41 (0.16), residues: 2343 helix: -0.90 (0.28), residues: 339 sheet: -1.06 (0.23), residues: 501 loop : -3.26 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.041 0.002 TYR B 173 PHE 0.021 0.002 PHE I 320 TRP 0.042 0.002 TRP B 427 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00420 (20371) covalent geometry : angle 0.87398 (27674) SS BOND : bond 0.00505 ( 30) SS BOND : angle 2.48122 ( 60) hydrogen bonds : bond 0.03826 ( 451) hydrogen bonds : angle 5.93311 ( 1239) link_ALPHA1-3 : bond 0.00651 ( 3) link_ALPHA1-3 : angle 3.01323 ( 9) link_ALPHA1-6 : bond 0.01341 ( 2) link_ALPHA1-6 : angle 1.78517 ( 6) link_BETA1-4 : bond 0.00767 ( 42) link_BETA1-4 : angle 3.34847 ( 126) link_NAG-ASN : bond 0.00549 ( 51) link_NAG-ASN : angle 3.79918 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 647 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8792 (mmt) cc_final: 0.8531 (mmp) REVERT: A 543 ASN cc_start: 0.9360 (t0) cc_final: 0.8486 (t0) REVERT: A 588 ARG cc_start: 0.8858 (tpt-90) cc_final: 0.8604 (tpt-90) REVERT: A 620 SER cc_start: 0.8718 (p) cc_final: 0.8019 (p) REVERT: B 96 TRP cc_start: 0.9412 (m100) cc_final: 0.8800 (m100) REVERT: B 106 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8293 (tm-30) REVERT: B 265 LEU cc_start: 0.9199 (mt) cc_final: 0.8912 (mm) REVERT: B 426 MET cc_start: 0.8889 (ppp) cc_final: 0.8483 (ppp) REVERT: B 485 LYS cc_start: 0.8842 (ptpt) cc_final: 0.8548 (ptpt) REVERT: B 492 GLU cc_start: 0.8695 (tp30) cc_final: 0.8197 (tp30) REVERT: C 588 ARG cc_start: 0.9105 (ttt90) cc_final: 0.8795 (tpt-90) REVERT: C 607 ASN cc_start: 0.8316 (t0) cc_final: 0.7967 (t0) REVERT: C 627 THR cc_start: 0.8431 (p) cc_final: 0.8218 (p) REVERT: C 654 GLU cc_start: 0.8313 (pt0) cc_final: 0.7938 (pt0) REVERT: C 658 GLN cc_start: 0.8611 (tp-100) cc_final: 0.7817 (tp40) REVERT: D 22 CYS cc_start: 0.7927 (t) cc_final: 0.7639 (t) REVERT: D 40 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8443 (tm-30) REVERT: D 52 ILE cc_start: 0.7204 (tp) cc_final: 0.6933 (tp) REVERT: D 58 THR cc_start: 0.8759 (m) cc_final: 0.8533 (m) REVERT: D 61 ASN cc_start: 0.8633 (t0) cc_final: 0.8422 (t0) REVERT: D 67 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7646 (mmm160) REVERT: E 31 PHE cc_start: 0.6711 (t80) cc_final: 0.6027 (t80) REVERT: E 60 ASP cc_start: 0.7810 (t0) cc_final: 0.7354 (t0) REVERT: E 92 ASP cc_start: 0.9084 (t0) cc_final: 0.8768 (t0) REVERT: E 104 LEU cc_start: 0.8207 (pt) cc_final: 0.7926 (pp) REVERT: F 522 PHE cc_start: 0.9134 (t80) cc_final: 0.8730 (t80) REVERT: F 523 LEU cc_start: 0.9356 (mt) cc_final: 0.9070 (mt) REVERT: F 543 ASN cc_start: 0.9162 (t0) cc_final: 0.8597 (t0) REVERT: F 588 ARG cc_start: 0.8530 (ttt180) cc_final: 0.8131 (tpt-90) REVERT: F 607 ASN cc_start: 0.7912 (t0) cc_final: 0.7404 (t0) REVERT: F 622 ILE cc_start: 0.9002 (mt) cc_final: 0.8796 (mt) REVERT: F 630 GLN cc_start: 0.8783 (mp10) cc_final: 0.7905 (mp10) REVERT: F 638 TYR cc_start: 0.8379 (m-10) cc_final: 0.8142 (m-10) REVERT: F 654 GLU cc_start: 0.8289 (pt0) cc_final: 0.8009 (tp30) REVERT: F 664 ASP cc_start: 0.6786 (p0) cc_final: 0.6516 (p0) REVERT: G 82 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8063 (mp10) REVERT: G 92 GLU cc_start: 0.7652 (pp20) cc_final: 0.7349 (pp20) REVERT: G 94 ASN cc_start: 0.8751 (t0) cc_final: 0.8105 (t0) REVERT: G 98 ASN cc_start: 0.8598 (t0) cc_final: 0.8394 (t0) REVERT: G 99 ASN cc_start: 0.9086 (p0) cc_final: 0.8761 (p0) REVERT: G 110 SER cc_start: 0.9495 (m) cc_final: 0.9250 (t) REVERT: G 113 ASP cc_start: 0.9418 (t0) cc_final: 0.9097 (t70) REVERT: G 156 GLN cc_start: 0.7824 (pp30) cc_final: 0.7264 (pm20) REVERT: G 164 GLU cc_start: 0.9019 (pp20) cc_final: 0.8739 (pp20) REVERT: G 166 ARG cc_start: 0.8435 (tmm-80) cc_final: 0.7996 (ttp80) REVERT: G 213 ILE cc_start: 0.9156 (mm) cc_final: 0.8950 (mt) REVERT: G 269 GLU cc_start: 0.8795 (tp30) cc_final: 0.8434 (tp30) REVERT: G 270 VAL cc_start: 0.9517 (p) cc_final: 0.9148 (p) REVERT: G 309 ILE cc_start: 0.9113 (mp) cc_final: 0.8879 (tp) REVERT: G 426 MET cc_start: 0.9052 (ppp) cc_final: 0.8794 (ppp) REVERT: H 47 GLU cc_start: 0.8205 (tp30) cc_final: 0.7914 (tp30) REVERT: H 48 TRP cc_start: 0.9199 (t60) cc_final: 0.8517 (t60) REVERT: I 50 THR cc_start: 0.9433 (p) cc_final: 0.9110 (p) REVERT: I 53 PHE cc_start: 0.8794 (p90) cc_final: 0.8566 (p90) REVERT: I 110 SER cc_start: 0.9427 (m) cc_final: 0.9129 (t) REVERT: I 181 VAL cc_start: 0.9810 (m) cc_final: 0.9581 (p) REVERT: I 195 ASN cc_start: 0.8122 (t0) cc_final: 0.7748 (t0) REVERT: I 211 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8291 (tm-30) REVERT: I 320 PHE cc_start: 0.7889 (t80) cc_final: 0.7558 (t80) REVERT: I 340 GLU cc_start: 0.9284 (tt0) cc_final: 0.8634 (tp30) REVERT: I 363 GLN cc_start: 0.8867 (pp30) cc_final: 0.8525 (pp30) REVERT: I 368 ASP cc_start: 0.7767 (t70) cc_final: 0.7519 (t70) REVERT: I 426 MET cc_start: 0.7687 (ptt) cc_final: 0.7278 (ptt) REVERT: I 477 ASP cc_start: 0.9281 (m-30) cc_final: 0.8981 (m-30) REVERT: J 40 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8228 (tm-30) REVERT: J 48 TRP cc_start: 0.9222 (t60) cc_final: 0.8641 (t60) REVERT: J 61 ASN cc_start: 0.8634 (t0) cc_final: 0.8036 (t0) REVERT: J 70 ILE cc_start: 0.9381 (mp) cc_final: 0.9179 (mm) REVERT: K 27 ASN cc_start: 0.8653 (t0) cc_final: 0.8430 (t0) REVERT: K 60 ASP cc_start: 0.8676 (t0) cc_final: 0.8125 (t0) REVERT: K 92 ASP cc_start: 0.8718 (t70) cc_final: 0.7840 (t70) REVERT: L 27 ASN cc_start: 0.8447 (t0) cc_final: 0.8217 (t0) REVERT: L 60 ASP cc_start: 0.8099 (t0) cc_final: 0.7691 (t0) REVERT: L 92 ASP cc_start: 0.8797 (t70) cc_final: 0.8014 (t70) outliers start: 2 outliers final: 1 residues processed: 649 average time/residue: 0.1308 time to fit residues: 134.8132 Evaluate side-chains 504 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 503 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 211 optimal weight: 0.0000 chunk 229 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN B 156 GLN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN G 33 ASN G 103 GLN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 ASN J 77 ASN L 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105038 restraints weight = 39582.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108275 restraints weight = 23557.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110546 restraints weight = 16272.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112121 restraints weight = 12409.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113228 restraints weight = 10188.970| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20499 Z= 0.137 Angle : 0.922 14.307 28028 Z= 0.417 Chirality : 0.053 0.476 3391 Planarity : 0.004 0.048 3389 Dihedral : 10.482 82.148 4566 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.35 % Favored : 88.60 % Rotamer: Outliers : 0.14 % Allowed : 0.96 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.35 (0.16), residues: 2343 helix: -0.91 (0.28), residues: 339 sheet: -0.98 (0.23), residues: 510 loop : -3.22 (0.14), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 617 TYR 0.046 0.002 TYR G 173 PHE 0.022 0.001 PHE I 320 TRP 0.056 0.002 TRP D 100B HIS 0.008 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00304 (20371) covalent geometry : angle 0.85395 (27674) SS BOND : bond 0.00487 ( 30) SS BOND : angle 2.15661 ( 60) hydrogen bonds : bond 0.03486 ( 451) hydrogen bonds : angle 5.83173 ( 1239) link_ALPHA1-3 : bond 0.00740 ( 3) link_ALPHA1-3 : angle 2.97648 ( 9) link_ALPHA1-6 : bond 0.01423 ( 2) link_ALPHA1-6 : angle 2.11554 ( 6) link_BETA1-4 : bond 0.00829 ( 42) link_BETA1-4 : angle 3.25994 ( 126) link_NAG-ASN : bond 0.00520 ( 51) link_NAG-ASN : angle 3.54499 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 653 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8738 (mmt) cc_final: 0.8516 (mmp) REVERT: A 543 ASN cc_start: 0.9171 (t0) cc_final: 0.8260 (t0) REVERT: A 588 ARG cc_start: 0.8714 (tpt-90) cc_final: 0.8021 (ttt180) REVERT: A 620 SER cc_start: 0.8630 (p) cc_final: 0.7902 (p) REVERT: A 622 ILE cc_start: 0.8948 (mm) cc_final: 0.8601 (mm) REVERT: B 96 TRP cc_start: 0.9401 (m100) cc_final: 0.8875 (m100) REVERT: B 233 PHE cc_start: 0.8459 (t80) cc_final: 0.8198 (t80) REVERT: B 265 LEU cc_start: 0.9181 (mt) cc_final: 0.8874 (mm) REVERT: B 474 ASP cc_start: 0.8571 (t70) cc_final: 0.8002 (t0) REVERT: B 475 MET cc_start: 0.7567 (mmm) cc_final: 0.7190 (tmm) REVERT: B 485 LYS cc_start: 0.8844 (ptpt) cc_final: 0.8537 (ptpt) REVERT: B 492 GLU cc_start: 0.8643 (tp30) cc_final: 0.8218 (tp30) REVERT: C 607 ASN cc_start: 0.8278 (t0) cc_final: 0.7943 (t0) REVERT: C 658 GLN cc_start: 0.8665 (tp-100) cc_final: 0.7835 (tp40) REVERT: D 22 CYS cc_start: 0.7730 (t) cc_final: 0.7467 (t) REVERT: D 40 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8227 (tm-30) REVERT: D 52 ILE cc_start: 0.7091 (tp) cc_final: 0.6666 (tp) REVERT: D 67 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7532 (mmm160) REVERT: E 38 GLN cc_start: 0.7232 (mm110) cc_final: 0.6827 (tp40) REVERT: E 60 ASP cc_start: 0.7850 (t0) cc_final: 0.7388 (t0) REVERT: E 104 LEU cc_start: 0.8169 (pt) cc_final: 0.7818 (pp) REVERT: F 522 PHE cc_start: 0.9138 (t80) cc_final: 0.8603 (t80) REVERT: F 523 LEU cc_start: 0.9257 (mt) cc_final: 0.8974 (mt) REVERT: F 543 ASN cc_start: 0.9168 (t0) cc_final: 0.8597 (t0) REVERT: F 607 ASN cc_start: 0.7681 (t0) cc_final: 0.7356 (t0) REVERT: F 620 SER cc_start: 0.8669 (m) cc_final: 0.8387 (m) REVERT: F 630 GLN cc_start: 0.8784 (mp10) cc_final: 0.8493 (mp10) REVERT: F 638 TYR cc_start: 0.8229 (m-10) cc_final: 0.7986 (m-10) REVERT: F 654 GLU cc_start: 0.8247 (pt0) cc_final: 0.7930 (tp30) REVERT: F 664 ASP cc_start: 0.6625 (p0) cc_final: 0.6278 (p0) REVERT: G 49 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8024 (tm-30) REVERT: G 82 GLN cc_start: 0.8809 (mm-40) cc_final: 0.7984 (mp10) REVERT: G 92 GLU cc_start: 0.7601 (pp20) cc_final: 0.7315 (pp20) REVERT: G 94 ASN cc_start: 0.8678 (t0) cc_final: 0.8057 (t0) REVERT: G 98 ASN cc_start: 0.8587 (t0) cc_final: 0.8339 (t0) REVERT: G 99 ASN cc_start: 0.9108 (p0) cc_final: 0.8738 (p0) REVERT: G 156 GLN cc_start: 0.7795 (pp30) cc_final: 0.7138 (pm20) REVERT: G 161 MET cc_start: 0.8538 (tpp) cc_final: 0.7774 (tpp) REVERT: G 166 ARG cc_start: 0.8441 (tmm-80) cc_final: 0.7975 (ttp80) REVERT: G 170 GLN cc_start: 0.6312 (mt0) cc_final: 0.5576 (mp10) REVERT: G 171 LYS cc_start: 0.9075 (ptmt) cc_final: 0.7696 (ptmt) REVERT: G 350 ARG cc_start: 0.8295 (tpt-90) cc_final: 0.7889 (tpt-90) REVERT: G 368 ASP cc_start: 0.7915 (t70) cc_final: 0.7700 (t0) REVERT: H 47 GLU cc_start: 0.8165 (tp30) cc_final: 0.7880 (tp30) REVERT: H 48 TRP cc_start: 0.9178 (t60) cc_final: 0.8465 (t60) REVERT: H 78 GLN cc_start: 0.7235 (mp10) cc_final: 0.6917 (mp10) REVERT: I 50 THR cc_start: 0.9416 (p) cc_final: 0.9109 (p) REVERT: I 53 PHE cc_start: 0.8760 (p90) cc_final: 0.8501 (p90) REVERT: I 110 SER cc_start: 0.9345 (m) cc_final: 0.9087 (t) REVERT: I 150 MET cc_start: 0.8582 (mpp) cc_final: 0.7545 (mpp) REVERT: I 181 VAL cc_start: 0.9803 (m) cc_final: 0.9557 (p) REVERT: I 211 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8253 (tm-30) REVERT: I 315 GLN cc_start: 0.8556 (mm-40) cc_final: 0.7567 (mp10) REVERT: I 320 PHE cc_start: 0.7724 (t80) cc_final: 0.7523 (t80) REVERT: I 340 GLU cc_start: 0.9194 (tt0) cc_final: 0.8558 (tp30) REVERT: I 363 GLN cc_start: 0.8806 (pp30) cc_final: 0.8487 (pp30) REVERT: I 368 ASP cc_start: 0.7663 (t70) cc_final: 0.7440 (t70) REVERT: I 426 MET cc_start: 0.7403 (ptt) cc_final: 0.7038 (ptt) REVERT: J 40 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8299 (tm-30) REVERT: J 48 TRP cc_start: 0.9256 (t60) cc_final: 0.8635 (t60) REVERT: J 52 ILE cc_start: 0.7731 (tp) cc_final: 0.7428 (tp) REVERT: J 61 ASN cc_start: 0.8524 (t0) cc_final: 0.7957 (t0) REVERT: J 70 ILE cc_start: 0.9206 (mp) cc_final: 0.8782 (tp) REVERT: K 51 ASN cc_start: 0.6855 (p0) cc_final: 0.6590 (p0) REVERT: K 60 ASP cc_start: 0.8795 (t0) cc_final: 0.8227 (t0) REVERT: K 92 ASP cc_start: 0.8675 (t70) cc_final: 0.7831 (t70) REVERT: L 60 ASP cc_start: 0.8203 (t0) cc_final: 0.7812 (t0) outliers start: 3 outliers final: 2 residues processed: 655 average time/residue: 0.1282 time to fit residues: 133.6072 Evaluate side-chains 521 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 519 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 53 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 0.0770 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102378 restraints weight = 40002.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105542 restraints weight = 23519.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107772 restraints weight = 16143.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109306 restraints weight = 12279.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110354 restraints weight = 10033.954| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20499 Z= 0.177 Angle : 0.946 13.882 28028 Z= 0.434 Chirality : 0.053 0.470 3391 Planarity : 0.005 0.050 3389 Dihedral : 10.506 79.471 4566 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.62 % Favored : 86.34 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.26 % 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: -3.36 (0.16), residues: 2343 helix: -0.74 (0.28), residues: 339 sheet: -1.06 (0.23), residues: 516 loop : -3.25 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 166 TYR 0.032 0.002 TYR G 173 PHE 0.021 0.002 PHE I 320 TRP 0.041 0.003 TRP B 427 HIS 0.008 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00409 (20371) covalent geometry : angle 0.87899 (27674) SS BOND : bond 0.00453 ( 30) SS BOND : angle 2.40585 ( 60) hydrogen bonds : bond 0.03677 ( 451) hydrogen bonds : angle 5.84744 ( 1239) link_ALPHA1-3 : bond 0.00604 ( 3) link_ALPHA1-3 : angle 2.93136 ( 9) link_ALPHA1-6 : bond 0.01385 ( 2) link_ALPHA1-6 : angle 2.17578 ( 6) link_BETA1-4 : bond 0.00746 ( 42) link_BETA1-4 : angle 3.23666 ( 126) link_NAG-ASN : bond 0.00464 ( 51) link_NAG-ASN : angle 3.55224 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 639 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8774 (mmt) cc_final: 0.8526 (mmp) REVERT: A 543 ASN cc_start: 0.9185 (t0) cc_final: 0.8299 (t0) REVERT: A 574 LYS cc_start: 0.8693 (mttt) cc_final: 0.8472 (mttt) REVERT: A 588 ARG cc_start: 0.8873 (tpt-90) cc_final: 0.8046 (ttt180) REVERT: B 92 GLU cc_start: 0.6564 (pp20) cc_final: 0.6085 (pp20) REVERT: B 96 TRP cc_start: 0.9372 (m100) cc_final: 0.8842 (m100) REVERT: B 205 CYS cc_start: 0.6449 (t) cc_final: 0.6132 (t) REVERT: B 233 PHE cc_start: 0.8610 (t80) cc_final: 0.8332 (t80) REVERT: B 265 LEU cc_start: 0.9261 (mt) cc_final: 0.8972 (mm) REVERT: B 320 PHE cc_start: 0.8453 (t80) cc_final: 0.8212 (t80) REVERT: B 475 MET cc_start: 0.7861 (mmm) cc_final: 0.7349 (mmm) REVERT: B 485 LYS cc_start: 0.8877 (ptpt) cc_final: 0.8620 (ptpt) REVERT: B 492 GLU cc_start: 0.8671 (tp30) cc_final: 0.8273 (tp30) REVERT: C 535 MET cc_start: 0.8619 (mmt) cc_final: 0.8413 (mmm) REVERT: C 538 THR cc_start: 0.8890 (p) cc_final: 0.8594 (p) REVERT: C 607 ASN cc_start: 0.8266 (t0) cc_final: 0.7931 (t0) REVERT: C 616 ASN cc_start: 0.8667 (p0) cc_final: 0.8434 (p0) REVERT: C 627 THR cc_start: 0.8567 (p) cc_final: 0.8295 (p) REVERT: D 22 CYS cc_start: 0.7401 (t) cc_final: 0.7175 (t) REVERT: D 40 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8378 (tm-30) REVERT: D 52 ILE cc_start: 0.7208 (tp) cc_final: 0.6935 (tp) REVERT: D 59 TYR cc_start: 0.7546 (m-80) cc_final: 0.7293 (m-10) REVERT: D 67 ARG cc_start: 0.8169 (mmm160) cc_final: 0.7614 (mmm160) REVERT: D 70 ILE cc_start: 0.9379 (mp) cc_final: 0.9137 (mm) REVERT: E 31 PHE cc_start: 0.6847 (t80) cc_final: 0.6288 (t80) REVERT: E 60 ASP cc_start: 0.7907 (t0) cc_final: 0.7499 (t0) REVERT: E 92 ASP cc_start: 0.8944 (t0) cc_final: 0.8009 (t70) REVERT: E 104 LEU cc_start: 0.8320 (pt) cc_final: 0.7974 (pp) REVERT: F 522 PHE cc_start: 0.9185 (t80) cc_final: 0.8778 (t80) REVERT: F 523 LEU cc_start: 0.9263 (mt) cc_final: 0.9002 (mt) REVERT: F 543 ASN cc_start: 0.9189 (t0) cc_final: 0.8695 (t0) REVERT: F 588 ARG cc_start: 0.8526 (ttt180) cc_final: 0.8122 (tpt-90) REVERT: F 607 ASN cc_start: 0.7655 (t0) cc_final: 0.7363 (t0) REVERT: F 622 ILE cc_start: 0.9029 (mt) cc_final: 0.8811 (mt) REVERT: F 630 GLN cc_start: 0.8892 (mp10) cc_final: 0.7949 (mp10) REVERT: F 638 TYR cc_start: 0.8382 (m-10) cc_final: 0.8103 (m-10) REVERT: F 654 GLU cc_start: 0.8294 (pt0) cc_final: 0.8004 (pt0) REVERT: F 664 ASP cc_start: 0.6729 (p0) cc_final: 0.6460 (p0) REVERT: G 82 GLN cc_start: 0.8819 (mm-40) cc_final: 0.7990 (mp10) REVERT: G 92 GLU cc_start: 0.7638 (pp20) cc_final: 0.7350 (pp20) REVERT: G 93 PHE cc_start: 0.8391 (m-80) cc_final: 0.7874 (m-80) REVERT: G 94 ASN cc_start: 0.8813 (t0) cc_final: 0.8180 (t0) REVERT: G 99 ASN cc_start: 0.9187 (p0) cc_final: 0.8832 (p0) REVERT: G 104 MET cc_start: 0.8971 (ttm) cc_final: 0.8114 (ttt) REVERT: G 110 SER cc_start: 0.9483 (m) cc_final: 0.9203 (t) REVERT: G 156 GLN cc_start: 0.7783 (pp30) cc_final: 0.7222 (pm20) REVERT: G 166 ARG cc_start: 0.8563 (tmm-80) cc_final: 0.8199 (ttp80) REVERT: G 171 LYS cc_start: 0.9024 (ptmt) cc_final: 0.8572 (ptmt) REVERT: G 350 ARG cc_start: 0.8329 (tpt-90) cc_final: 0.7989 (tpt-90) REVERT: H 47 GLU cc_start: 0.8267 (tp30) cc_final: 0.8000 (tp30) REVERT: H 48 TRP cc_start: 0.9131 (t60) cc_final: 0.8414 (t60) REVERT: I 50 THR cc_start: 0.9409 (p) cc_final: 0.9086 (p) REVERT: I 53 PHE cc_start: 0.8879 (p90) cc_final: 0.8649 (p90) REVERT: I 94 ASN cc_start: 0.8835 (t0) cc_final: 0.8614 (t0) REVERT: I 106 GLU cc_start: 0.9153 (tt0) cc_final: 0.8798 (tt0) REVERT: I 110 SER cc_start: 0.9379 (m) cc_final: 0.9155 (t) REVERT: I 150 MET cc_start: 0.8588 (mpp) cc_final: 0.7159 (mpp) REVERT: I 174 SER cc_start: 0.8791 (m) cc_final: 0.8153 (p) REVERT: I 181 VAL cc_start: 0.9800 (m) cc_final: 0.9553 (p) REVERT: I 195 ASN cc_start: 0.8079 (t0) cc_final: 0.7677 (t0) REVERT: I 211 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8273 (tm-30) REVERT: I 320 PHE cc_start: 0.7877 (t80) cc_final: 0.7634 (t80) REVERT: I 328 MET cc_start: 0.7443 (ptm) cc_final: 0.6889 (ptp) REVERT: I 340 GLU cc_start: 0.9155 (tt0) cc_final: 0.8415 (tp30) REVERT: I 368 ASP cc_start: 0.7734 (t70) cc_final: 0.7476 (t70) REVERT: I 426 MET cc_start: 0.7572 (ptt) cc_final: 0.7128 (ptt) REVERT: I 477 ASP cc_start: 0.9226 (m-30) cc_final: 0.8938 (m-30) REVERT: I 479 TRP cc_start: 0.9139 (m-90) cc_final: 0.8918 (m-90) REVERT: I 499 THR cc_start: 0.8642 (t) cc_final: 0.8418 (t) REVERT: J 40 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8235 (tm-30) REVERT: J 48 TRP cc_start: 0.9299 (t60) cc_final: 0.8736 (t60) REVERT: J 61 ASN cc_start: 0.8660 (t0) cc_final: 0.8060 (t0) REVERT: K 51 ASN cc_start: 0.6887 (p0) cc_final: 0.6664 (p0) REVERT: K 60 ASP cc_start: 0.8740 (t0) cc_final: 0.8139 (t0) REVERT: K 92 ASP cc_start: 0.8709 (t70) cc_final: 0.7829 (t70) REVERT: L 27 ASN cc_start: 0.8442 (t0) cc_final: 0.8173 (t0) REVERT: L 60 ASP cc_start: 0.8252 (t0) cc_final: 0.7736 (t0) REVERT: L 92 ASP cc_start: 0.8832 (t70) cc_final: 0.8044 (t70) outliers start: 1 outliers final: 0 residues processed: 639 average time/residue: 0.1250 time to fit residues: 126.6986 Evaluate side-chains 527 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 25 optimal weight: 0.0000 chunk 229 optimal weight: 0.0370 chunk 4 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 139 optimal weight: 0.0570 chunk 59 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 152 optimal weight: 0.0570 chunk 154 optimal weight: 5.9990 overall best weight: 0.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN E 17 GLN E 51 ASN G 137 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN L 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106878 restraints weight = 39340.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110190 restraints weight = 23171.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112528 restraints weight = 15867.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114165 restraints weight = 11999.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115292 restraints weight = 9754.942| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20499 Z= 0.142 Angle : 0.935 14.224 28028 Z= 0.424 Chirality : 0.053 0.478 3391 Planarity : 0.004 0.048 3389 Dihedral : 10.249 81.288 4566 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.31 % Favored : 88.65 % Rotamer: Outliers : 0.14 % Allowed : 0.38 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.23 (0.16), residues: 2343 helix: -0.63 (0.28), residues: 330 sheet: -0.97 (0.23), residues: 516 loop : -3.15 (0.14), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 273 TYR 0.028 0.002 TYR G 173 PHE 0.019 0.001 PHE I 320 TRP 0.084 0.002 TRP G 96 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00314 (20371) covalent geometry : angle 0.87047 (27674) SS BOND : bond 0.00568 ( 30) SS BOND : angle 2.08968 ( 60) hydrogen bonds : bond 0.03328 ( 451) hydrogen bonds : angle 5.67703 ( 1239) link_ALPHA1-3 : bond 0.00761 ( 3) link_ALPHA1-3 : angle 2.78943 ( 9) link_ALPHA1-6 : bond 0.01396 ( 2) link_ALPHA1-6 : angle 2.23250 ( 6) link_BETA1-4 : bond 0.00808 ( 42) link_BETA1-4 : angle 3.14785 ( 126) link_NAG-ASN : bond 0.00534 ( 51) link_NAG-ASN : angle 3.55442 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3613.64 seconds wall clock time: 63 minutes 24.41 seconds (3804.41 seconds total)