Starting phenix.real_space_refine on Sun Aug 24 12:46:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tl3_41360/08_2025/8tl3_41360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tl3_41360/08_2025/8tl3_41360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tl3_41360/08_2025/8tl3_41360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tl3_41360/08_2025/8tl3_41360.map" model { file = "/net/cci-nas-00/data/ceres_data/8tl3_41360/08_2025/8tl3_41360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tl3_41360/08_2025/8tl3_41360.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 12555 2.51 5 N 3366 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20070 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "G" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 973 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 861 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "I" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 973 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "J" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 861 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "K" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 973 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 861 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "R" 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: "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: "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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.11, per 1000 atoms: 0.25 Number of scatterers: 20070 At special positions: 0 Unit cell: (145.965, 153.739, 126.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 4020 8.00 N 3366 7.00 C 12555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN Y 4 " - " MAN Y 5 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA Y 3 " - " MAN Y 4 " " BMA j 3 " - " MAN j 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 88 " " NAG A 606 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 88 " " NAG C 606 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 88 " " NAG E 606 " - " ASN E 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 363 " " NAG U 1 " - " ASN C 448 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 295 " " NAG d 1 " - " ASN C 363 " " NAG e 1 " - " ASN E 295 " " NAG f 1 " - " ASN E 448 " " NAG g 1 " - " ASN E 160 " " NAG h 1 " - " ASN E 276 " " NAG i 1 " - " ASN E 386 " " NAG j 1 " - " ASN E 262 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 332 " " NAG m 1 " - " ASN E 363 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 867.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4494 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 44 sheets defined 19.0% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.156A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.671A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.813A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.534A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 4.124A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.669A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.809A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.463A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.688A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.780A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.584A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 546 removed outlier: 4.032A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.558A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.749A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 removed outlier: 3.758A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.422A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 removed outlier: 3.583A pdb=" N MET E 150 " --> pdb=" O THR E 139 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG E 151 " --> pdb=" O ASP E 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 139 through 151' Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.787A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 481 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 546 removed outlier: 4.079A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER F 546 " --> pdb=" O ARG F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.573A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.759A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 65 removed outlier: 4.442A pdb=" N SER G 65 " --> pdb=" O PRO G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.792A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.767A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 removed outlier: 4.456A pdb=" N SER K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.784A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.520A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.040A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.648A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.568A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.620A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.190A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.620A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.485A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 516 through 519 removed outlier: 6.497A pdb=" N GLY B 516 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N TYR G 99 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 518 " --> pdb=" O TYR G 99 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN G 95 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR G 34 " --> pdb=" O GLN G 95 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP G 35 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN G 50 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.687A pdb=" N SER G 100F" --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL G 100 " --> pdb=" O LEU G 100D" (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU G 100D" --> pdb=" O VAL G 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.305A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.880A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.574A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.504A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.667A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.140A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.667A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.504A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.525A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 516 through 519 removed outlier: 6.410A pdb=" N GLY D 516 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR I 99 " --> pdb=" O GLY D 516 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL D 518 " --> pdb=" O TYR I 99 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN I 95 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR I 34 " --> pdb=" O GLN I 95 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP I 35 " --> pdb=" O ASN I 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.697A pdb=" N SER I 100F" --> pdb=" O THR I 98 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL I 100 " --> pdb=" O LEU I 100D" (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU I 100D" --> pdb=" O VAL I 100 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.215A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.826A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.706A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.598A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.433A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.312A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.433A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.564A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 516 through 519 removed outlier: 3.969A pdb=" N GLY F 516 " --> pdb=" O GLN K 95 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP K 35 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN K 50 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.754A pdb=" N SER K 100F" --> pdb=" O THR K 98 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL K 100 " --> pdb=" O LEU K 100D" (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU K 100D" --> pdb=" O VAL K 100 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.551A pdb=" N ASP H 105 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.551A pdb=" N ASP H 105 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN H 90 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.531A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.531A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN J 90 " --> pdb=" O THR J 97 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.507A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.507A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6358 1.35 - 1.48: 5339 1.48 - 1.60: 8607 1.60 - 1.73: 0 1.73 - 1.85: 174 Bond restraints: 20478 Sorted by residual: bond pdb=" C ARG C 298 " pdb=" N PRO C 299 " ideal model delta sigma weight residual 1.336 1.357 -0.021 9.80e-03 1.04e+04 4.71e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.32e+00 bond pdb=" C1 NAG f 1 " pdb=" O5 NAG f 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 ... (remaining 20473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 26762 1.41 - 2.82: 846 2.82 - 4.23: 172 4.23 - 5.65: 36 5.65 - 7.06: 15 Bond angle restraints: 27831 Sorted by residual: angle pdb=" CA ASN D 607 " pdb=" CB ASN D 607 " pdb=" CG ASN D 607 " ideal model delta sigma weight residual 112.60 115.81 -3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" CA CYS A 247 " pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 114.40 121.34 -6.94 2.30e+00 1.89e-01 9.12e+00 angle pdb=" CA CYS C 418 " pdb=" CB CYS C 418 " pdb=" SG CYS C 418 " ideal model delta sigma weight residual 114.40 120.86 -6.46 2.30e+00 1.89e-01 7.89e+00 angle pdb=" N CYS A 247 " pdb=" CA CYS A 247 " pdb=" C CYS A 247 " ideal model delta sigma weight residual 107.88 111.79 -3.91 1.41e+00 5.03e-01 7.71e+00 angle pdb=" CG LYS A 232 " pdb=" CD LYS A 232 " pdb=" CE LYS A 232 " ideal model delta sigma weight residual 111.30 117.46 -6.16 2.30e+00 1.89e-01 7.18e+00 ... (remaining 27826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.70: 12105 21.70 - 43.39: 953 43.39 - 65.09: 177 65.09 - 86.79: 40 86.79 - 108.49: 15 Dihedral angle restraints: 13290 sinusoidal: 6318 harmonic: 6972 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 3.17 -89.17 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 6.55 86.45 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 9.31 83.69 1 1.00e+01 1.00e-02 8.55e+01 ... (remaining 13287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2857 0.059 - 0.117: 408 0.117 - 0.176: 95 0.176 - 0.235: 0 0.235 - 0.294: 6 Chirality restraints: 3366 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.57e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3363 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 205 " 0.052 5.00e-02 4.00e+02 7.75e-02 9.60e+00 pdb=" N PRO C 206 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 206 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 206 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 205 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO A 206 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 205 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO E 206 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO E 206 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 206 " -0.033 5.00e-02 4.00e+02 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 138 2.62 - 3.19: 16140 3.19 - 3.76: 28216 3.76 - 4.33: 40347 4.33 - 4.90: 69332 Nonbonded interactions: 154173 Sorted by model distance: nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.049 3.040 nonbonded pdb=" O LEU E 369 " pdb=" OG1 THR E 373 " model vdw 2.124 3.040 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.130 3.040 nonbonded pdb=" OG1 THR H 30 " pdb=" OD1 ASP H 32 " model vdw 2.263 3.040 nonbonded pdb=" O3 NAG l 1 " pdb=" O5 NAG l 2 " model vdw 2.279 3.040 ... (remaining 154168 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 'Q' selection = chain 'Y' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.750 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.310 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 0.004 0.043 20601 Z= 0.203 Angle : 0.645 7.058 28158 Z= 0.302 Chirality : 0.047 0.294 3366 Planarity : 0.004 0.077 3447 Dihedral : 15.470 108.486 8670 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.94 % Rotamer: Outliers : 0.19 % Allowed : 10.72 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.18), residues: 2373 helix: 2.30 (0.28), residues: 408 sheet: 0.52 (0.18), residues: 795 loop : -0.36 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 444 TYR 0.010 0.001 TYR A 191 PHE 0.010 0.001 PHE C 382 TRP 0.007 0.001 TRP L 35 HIS 0.004 0.000 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00421 (20478) covalent geometry : angle 0.62252 (27831) SS BOND : bond 0.00577 ( 42) SS BOND : angle 1.90278 ( 84) hydrogen bonds : bond 0.09537 ( 739) hydrogen bonds : angle 5.42271 ( 2034) link_ALPHA1-2 : bond 0.00350 ( 3) link_ALPHA1-2 : angle 1.61998 ( 9) link_ALPHA1-3 : bond 0.00508 ( 3) link_ALPHA1-3 : angle 1.43869 ( 9) link_BETA1-4 : bond 0.00434 ( 30) link_BETA1-4 : angle 0.89017 ( 90) link_NAG-ASN : bond 0.00269 ( 45) link_NAG-ASN : angle 1.96294 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.8131 (tt) cc_final: 0.7889 (tt) REVERT: B 601 LYS cc_start: 0.8917 (mttp) cc_final: 0.8565 (mtmt) REVERT: F 653 GLN cc_start: 0.8017 (mt0) cc_final: 0.7700 (tt0) REVERT: K 82 MET cc_start: 0.4227 (mmm) cc_final: 0.2749 (ptm) outliers start: 4 outliers final: 1 residues processed: 175 average time/residue: 0.1685 time to fit residues: 43.5405 Evaluate side-chains 169 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 355 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.0040 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 30.0000 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 616 ASN C 195 ASN C 246 GLN D 540 GLN D 616 ASN D 653 GLN D 658 GLN E 94 ASN E 355 ASN F 658 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.194550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.133606 restraints weight = 20289.018| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.92 r_work: 0.2813 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20601 Z= 0.160 Angle : 0.624 9.540 28158 Z= 0.306 Chirality : 0.045 0.274 3366 Planarity : 0.004 0.057 3447 Dihedral : 8.116 75.874 4268 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.85 % Favored : 98.10 % Rotamer: Outliers : 1.83 % Allowed : 10.06 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.17), residues: 2373 helix: 2.03 (0.28), residues: 408 sheet: 0.66 (0.18), residues: 747 loop : -0.58 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 444 TYR 0.011 0.001 TYR A 486 PHE 0.020 0.002 PHE A 383 TRP 0.012 0.001 TRP E 45 HIS 0.005 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00387 (20478) covalent geometry : angle 0.59295 (27831) SS BOND : bond 0.00565 ( 42) SS BOND : angle 1.63440 ( 84) hydrogen bonds : bond 0.04827 ( 739) hydrogen bonds : angle 4.55949 ( 2034) link_ALPHA1-2 : bond 0.00683 ( 3) link_ALPHA1-2 : angle 1.72560 ( 9) link_ALPHA1-3 : bond 0.01165 ( 3) link_ALPHA1-3 : angle 2.25195 ( 9) link_BETA1-4 : bond 0.00806 ( 30) link_BETA1-4 : angle 1.11397 ( 90) link_NAG-ASN : bond 0.00315 ( 45) link_NAG-ASN : angle 2.36570 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 601 LYS cc_start: 0.8945 (mttp) cc_final: 0.8600 (mtmt) REVERT: C 360 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.7970 (ttp80) REVERT: E 475 MET cc_start: 0.8481 (tpp) cc_final: 0.8253 (mmp) REVERT: F 633 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8279 (mttt) REVERT: F 653 GLN cc_start: 0.8059 (mt0) cc_final: 0.7337 (tt0) REVERT: I 76 ASN cc_start: 0.4787 (OUTLIER) cc_final: 0.4566 (m110) REVERT: K 82 MET cc_start: 0.4264 (mmm) cc_final: 0.2205 (ptm) outliers start: 39 outliers final: 17 residues processed: 216 average time/residue: 0.1564 time to fit residues: 50.4225 Evaluate side-chains 192 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 236 optimal weight: 20.0000 chunk 170 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 81 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 133 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 184 optimal weight: 30.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 616 ASN C 246 GLN C 355 ASN D 616 ASN E 355 ASN F 652 GLN F 653 GLN F 658 GLN K 35AASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.192386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.130357 restraints weight = 20282.606| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.90 r_work: 0.2799 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20601 Z= 0.133 Angle : 0.576 10.857 28158 Z= 0.283 Chirality : 0.044 0.266 3366 Planarity : 0.004 0.054 3447 Dihedral : 6.701 59.704 4266 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.23 % Favored : 97.72 % Rotamer: Outliers : 1.93 % Allowed : 11.61 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.17), residues: 2373 helix: 1.89 (0.28), residues: 408 sheet: 0.68 (0.18), residues: 774 loop : -0.70 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.009 0.001 TYR I 91 PHE 0.017 0.001 PHE A 383 TRP 0.009 0.001 TRP E 45 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00320 (20478) covalent geometry : angle 0.54315 (27831) SS BOND : bond 0.00499 ( 42) SS BOND : angle 1.57691 ( 84) hydrogen bonds : bond 0.04566 ( 739) hydrogen bonds : angle 4.45417 ( 2034) link_ALPHA1-2 : bond 0.00453 ( 3) link_ALPHA1-2 : angle 1.52383 ( 9) link_ALPHA1-3 : bond 0.01100 ( 3) link_ALPHA1-3 : angle 1.50364 ( 9) link_BETA1-4 : bond 0.00513 ( 30) link_BETA1-4 : angle 1.14904 ( 90) link_NAG-ASN : bond 0.00233 ( 45) link_NAG-ASN : angle 2.39277 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8286 (mtt90) REVERT: A 381 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8301 (mm-30) REVERT: B 601 LYS cc_start: 0.8891 (mttp) cc_final: 0.8498 (mtmt) REVERT: C 360 ARG cc_start: 0.8539 (mmm-85) cc_final: 0.7972 (ttp80) REVERT: C 502 LYS cc_start: 0.8453 (ptmm) cc_final: 0.8072 (tttm) REVERT: F 633 LYS cc_start: 0.8616 (ttmm) cc_final: 0.8361 (mttt) REVERT: F 653 GLN cc_start: 0.8071 (mt0) cc_final: 0.7278 (tt0) REVERT: K 82 MET cc_start: 0.4231 (mmm) cc_final: 0.2208 (ptm) outliers start: 41 outliers final: 23 residues processed: 210 average time/residue: 0.1562 time to fit residues: 48.5847 Evaluate side-chains 198 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain G residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 56 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 217 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 239 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 616 ASN C 246 GLN C 355 ASN D 616 ASN D 652 GLN E 85 HIS E 355 ASN F 591 GLN F 607 ASN F 652 GLN F 658 GLN I 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.189757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.137984 restraints weight = 20300.514| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.76 r_work: 0.2894 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20601 Z= 0.167 Angle : 0.628 10.681 28158 Z= 0.306 Chirality : 0.045 0.280 3366 Planarity : 0.004 0.055 3447 Dihedral : 6.138 54.829 4266 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.60 % Rotamer: Outliers : 2.68 % Allowed : 11.75 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 0.21 (0.17), residues: 2373 helix: 1.69 (0.28), residues: 408 sheet: 0.62 (0.18), residues: 780 loop : -0.73 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.010 0.001 TYR I 91 PHE 0.020 0.002 PHE A 383 TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00413 (20478) covalent geometry : angle 0.59451 (27831) SS BOND : bond 0.00638 ( 42) SS BOND : angle 1.77081 ( 84) hydrogen bonds : bond 0.05180 ( 739) hydrogen bonds : angle 4.47922 ( 2034) link_ALPHA1-2 : bond 0.00410 ( 3) link_ALPHA1-2 : angle 1.60058 ( 9) link_ALPHA1-3 : bond 0.01074 ( 3) link_ALPHA1-3 : angle 1.85481 ( 9) link_BETA1-4 : bond 0.00548 ( 30) link_BETA1-4 : angle 1.23813 ( 90) link_NAG-ASN : bond 0.00249 ( 45) link_NAG-ASN : angle 2.47208 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 174 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8355 (mtt90) REVERT: B 601 LYS cc_start: 0.8941 (mttp) cc_final: 0.8506 (mtmt) REVERT: C 492 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: C 502 LYS cc_start: 0.8751 (ptmm) cc_final: 0.8432 (tttm) REVERT: D 654 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: E 191 TYR cc_start: 0.9349 (m-80) cc_final: 0.9105 (m-80) REVERT: F 633 LYS cc_start: 0.8651 (ttmm) cc_final: 0.8394 (mttt) REVERT: K 82 MET cc_start: 0.4416 (mmm) cc_final: 0.2365 (ptm) outliers start: 57 outliers final: 32 residues processed: 216 average time/residue: 0.1511 time to fit residues: 48.8455 Evaluate side-chains 206 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain F residue 607 ASN Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 199 optimal weight: 6.9990 chunk 182 optimal weight: 8.9990 chunk 74 optimal weight: 0.0970 chunk 168 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 222 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 190 optimal weight: 20.0000 chunk 160 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN C 67 ASN C 246 GLN C 355 ASN D 616 ASN E 355 ASN F 653 GLN J 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.187361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.133475 restraints weight = 20293.803| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.81 r_work: 0.2803 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20601 Z= 0.226 Angle : 0.712 13.024 28158 Z= 0.344 Chirality : 0.048 0.294 3366 Planarity : 0.005 0.057 3447 Dihedral : 5.982 58.194 4266 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.57 % Favored : 97.30 % Rotamer: Outliers : 2.77 % Allowed : 12.79 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.17), residues: 2373 helix: 1.37 (0.28), residues: 408 sheet: 0.55 (0.18), residues: 780 loop : -0.86 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.011 0.002 TYR E 384 PHE 0.022 0.002 PHE A 383 TRP 0.013 0.002 TRP A 427 HIS 0.004 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00575 (20478) covalent geometry : angle 0.67783 (27831) SS BOND : bond 0.00658 ( 42) SS BOND : angle 1.94507 ( 84) hydrogen bonds : bond 0.06175 ( 739) hydrogen bonds : angle 4.62310 ( 2034) link_ALPHA1-2 : bond 0.00343 ( 3) link_ALPHA1-2 : angle 1.74374 ( 9) link_ALPHA1-3 : bond 0.01000 ( 3) link_ALPHA1-3 : angle 1.82974 ( 9) link_BETA1-4 : bond 0.00579 ( 30) link_BETA1-4 : angle 1.35462 ( 90) link_NAG-ASN : bond 0.00304 ( 45) link_NAG-ASN : angle 2.64866 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 169 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8438 (mtt90) REVERT: B 601 LYS cc_start: 0.8974 (mttp) cc_final: 0.8513 (mtmt) REVERT: C 492 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8486 (mt-10) REVERT: C 500 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.7827 (mtm-85) REVERT: C 502 LYS cc_start: 0.8890 (ptmm) cc_final: 0.8684 (tttm) REVERT: D 654 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: K 82 MET cc_start: 0.4390 (mmm) cc_final: 0.2369 (ptm) outliers start: 59 outliers final: 37 residues processed: 213 average time/residue: 0.1502 time to fit residues: 47.8678 Evaluate side-chains 207 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 152 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 190 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 184 optimal weight: 30.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 355 ASN B 616 ASN C 355 ASN E 355 ASN F 653 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.190515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.106077 restraints weight = 20078.074| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.68 r_work: 0.2682 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20601 Z= 0.147 Angle : 0.616 11.070 28158 Z= 0.301 Chirality : 0.044 0.287 3366 Planarity : 0.004 0.056 3447 Dihedral : 5.615 59.828 4266 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.49 % Favored : 97.39 % Rotamer: Outliers : 2.59 % Allowed : 13.31 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.17), residues: 2373 helix: 1.49 (0.28), residues: 408 sheet: 0.62 (0.18), residues: 774 loop : -0.89 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.010 0.001 TYR I 91 PHE 0.018 0.001 PHE C 383 TRP 0.013 0.001 TRP A 427 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00357 (20478) covalent geometry : angle 0.57905 (27831) SS BOND : bond 0.00596 ( 42) SS BOND : angle 1.83561 ( 84) hydrogen bonds : bond 0.05128 ( 739) hydrogen bonds : angle 4.47693 ( 2034) link_ALPHA1-2 : bond 0.00297 ( 3) link_ALPHA1-2 : angle 1.70564 ( 9) link_ALPHA1-3 : bond 0.01063 ( 3) link_ALPHA1-3 : angle 1.81688 ( 9) link_BETA1-4 : bond 0.00532 ( 30) link_BETA1-4 : angle 1.27002 ( 90) link_NAG-ASN : bond 0.00254 ( 45) link_NAG-ASN : angle 2.55319 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8283 (mtt90) REVERT: A 358 ILE cc_start: 0.7570 (mm) cc_final: 0.7326 (mm) REVERT: B 601 LYS cc_start: 0.8881 (mttp) cc_final: 0.8483 (mtmt) REVERT: C 492 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: C 500 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7662 (mtm-85) REVERT: C 502 LYS cc_start: 0.8837 (ptmm) cc_final: 0.8633 (tttm) REVERT: D 654 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7060 (mt-10) REVERT: E 117 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8074 (mttp) REVERT: G 100 SER cc_start: 0.7608 (OUTLIER) cc_final: 0.6845 (p) REVERT: K 82 MET cc_start: 0.3566 (mmm) cc_final: 0.2038 (ptm) outliers start: 55 outliers final: 31 residues processed: 212 average time/residue: 0.1612 time to fit residues: 50.9585 Evaluate side-chains 203 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 377 ASN B 616 ASN C 355 ASN E 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.186870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.115283 restraints weight = 20284.602| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.04 r_work: 0.2643 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 20601 Z= 0.220 Angle : 0.719 12.631 28158 Z= 0.347 Chirality : 0.048 0.305 3366 Planarity : 0.005 0.057 3447 Dihedral : 5.645 55.904 4266 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.74 % Favored : 97.18 % Rotamer: Outliers : 2.73 % Allowed : 13.54 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.17), residues: 2373 helix: 1.27 (0.28), residues: 408 sheet: 0.47 (0.18), residues: 783 loop : -0.96 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 444 TYR 0.011 0.002 TYR I 91 PHE 0.021 0.002 PHE E 383 TRP 0.014 0.002 TRP A 427 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00557 (20478) covalent geometry : angle 0.68259 (27831) SS BOND : bond 0.00744 ( 42) SS BOND : angle 2.13831 ( 84) hydrogen bonds : bond 0.06298 ( 739) hydrogen bonds : angle 4.63754 ( 2034) link_ALPHA1-2 : bond 0.00288 ( 3) link_ALPHA1-2 : angle 1.85625 ( 9) link_ALPHA1-3 : bond 0.00981 ( 3) link_ALPHA1-3 : angle 1.77268 ( 9) link_BETA1-4 : bond 0.00577 ( 30) link_BETA1-4 : angle 1.37324 ( 90) link_NAG-ASN : bond 0.00326 ( 45) link_NAG-ASN : angle 2.69421 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8271 (mtt90) REVERT: A 358 ILE cc_start: 0.7764 (mm) cc_final: 0.7513 (mm) REVERT: B 601 LYS cc_start: 0.8925 (mttp) cc_final: 0.8586 (mtmt) REVERT: B 619 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7988 (mp) REVERT: C 492 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8286 (mt-10) REVERT: C 500 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7737 (mtm180) REVERT: D 654 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: G 100 SER cc_start: 0.7569 (OUTLIER) cc_final: 0.6771 (p) REVERT: K 82 MET cc_start: 0.3656 (mmm) cc_final: 0.2045 (ptm) outliers start: 58 outliers final: 40 residues processed: 213 average time/residue: 0.1569 time to fit residues: 50.0213 Evaluate side-chains 214 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 146 optimal weight: 0.1980 chunk 197 optimal weight: 9.9990 chunk 225 optimal weight: 20.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 616 ASN C 355 ASN H 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.187255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.115905 restraints weight = 20235.353| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.11 r_work: 0.2629 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 20601 Z= 0.204 Angle : 0.693 12.755 28158 Z= 0.336 Chirality : 0.047 0.304 3366 Planarity : 0.005 0.058 3447 Dihedral : 5.555 53.381 4266 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 2.54 % Allowed : 14.25 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.17), residues: 2373 helix: 1.25 (0.28), residues: 408 sheet: 0.51 (0.18), residues: 780 loop : -0.99 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 444 TYR 0.011 0.002 TYR I 91 PHE 0.022 0.002 PHE A 383 TRP 0.014 0.002 TRP E 427 HIS 0.003 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00515 (20478) covalent geometry : angle 0.65601 (27831) SS BOND : bond 0.00709 ( 42) SS BOND : angle 2.09881 ( 84) hydrogen bonds : bond 0.05987 ( 739) hydrogen bonds : angle 4.60480 ( 2034) link_ALPHA1-2 : bond 0.00246 ( 3) link_ALPHA1-2 : angle 1.85315 ( 9) link_ALPHA1-3 : bond 0.00982 ( 3) link_ALPHA1-3 : angle 1.70112 ( 9) link_BETA1-4 : bond 0.00549 ( 30) link_BETA1-4 : angle 1.35013 ( 90) link_NAG-ASN : bond 0.00294 ( 45) link_NAG-ASN : angle 2.65851 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 167 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8780 (mt) REVERT: A 151 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8256 (mtt90) REVERT: A 358 ILE cc_start: 0.7713 (mm) cc_final: 0.7434 (mm) REVERT: B 601 LYS cc_start: 0.8929 (mttp) cc_final: 0.8595 (mtmt) REVERT: B 619 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7959 (mp) REVERT: C 492 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: C 500 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7702 (mtm-85) REVERT: D 619 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8383 (mp) REVERT: D 654 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: G 100 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.6898 (p) REVERT: K 82 MET cc_start: 0.3657 (mmm) cc_final: 0.2031 (ptm) outliers start: 54 outliers final: 40 residues processed: 209 average time/residue: 0.1512 time to fit residues: 46.9470 Evaluate side-chains 212 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 27 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 193 optimal weight: 30.0000 chunk 172 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 575 GLN B 616 ASN C 355 ASN G 71 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.187502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.102764 restraints weight = 20068.026| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.60 r_work: 0.2675 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 20601 Z= 0.223 Angle : 0.717 12.845 28158 Z= 0.347 Chirality : 0.048 0.308 3366 Planarity : 0.005 0.058 3447 Dihedral : 5.570 51.930 4266 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 2.68 % Allowed : 14.29 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.17), residues: 2373 helix: 1.20 (0.28), residues: 408 sheet: 0.44 (0.18), residues: 786 loop : -0.99 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 444 TYR 0.011 0.002 TYR I 91 PHE 0.022 0.002 PHE A 383 TRP 0.015 0.002 TRP E 427 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00566 (20478) covalent geometry : angle 0.68008 (27831) SS BOND : bond 0.00730 ( 42) SS BOND : angle 2.13715 ( 84) hydrogen bonds : bond 0.06245 ( 739) hydrogen bonds : angle 4.62507 ( 2034) link_ALPHA1-2 : bond 0.00237 ( 3) link_ALPHA1-2 : angle 1.90748 ( 9) link_ALPHA1-3 : bond 0.00947 ( 3) link_ALPHA1-3 : angle 1.63984 ( 9) link_BETA1-4 : bond 0.00556 ( 30) link_BETA1-4 : angle 1.38265 ( 90) link_NAG-ASN : bond 0.00306 ( 45) link_NAG-ASN : angle 2.68410 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8774 (mt) REVERT: A 151 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8260 (mtt90) REVERT: A 358 ILE cc_start: 0.7666 (mm) cc_final: 0.7378 (mm) REVERT: B 601 LYS cc_start: 0.8907 (mttp) cc_final: 0.8587 (mtmt) REVERT: B 619 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7885 (mp) REVERT: C 211 GLU cc_start: 0.7339 (tp30) cc_final: 0.7124 (tp30) REVERT: C 492 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8419 (mt-10) REVERT: C 500 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7584 (mtm180) REVERT: D 619 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8333 (mp) REVERT: D 654 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: G 100 SER cc_start: 0.7621 (OUTLIER) cc_final: 0.6853 (p) REVERT: K 82 MET cc_start: 0.3554 (mmm) cc_final: 0.2003 (ptm) outliers start: 57 outliers final: 43 residues processed: 212 average time/residue: 0.1497 time to fit residues: 47.4263 Evaluate side-chains 218 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 97 ARG Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 135 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 144 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 616 ASN C 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.192434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.114458 restraints weight = 20207.862| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.56 r_work: 0.2763 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20601 Z= 0.116 Angle : 0.584 11.761 28158 Z= 0.287 Chirality : 0.043 0.291 3366 Planarity : 0.004 0.055 3447 Dihedral : 5.213 53.416 4266 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.61 % Favored : 97.30 % Rotamer: Outliers : 1.88 % Allowed : 15.19 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.17), residues: 2373 helix: 1.59 (0.28), residues: 408 sheet: 0.67 (0.18), residues: 783 loop : -0.89 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 444 TYR 0.011 0.001 TYR K 34 PHE 0.017 0.001 PHE A 53 TRP 0.018 0.001 TRP E 427 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00270 (20478) covalent geometry : angle 0.54573 (27831) SS BOND : bond 0.00560 ( 42) SS BOND : angle 1.74614 ( 84) hydrogen bonds : bond 0.04551 ( 739) hydrogen bonds : angle 4.39742 ( 2034) link_ALPHA1-2 : bond 0.00228 ( 3) link_ALPHA1-2 : angle 1.75849 ( 9) link_ALPHA1-3 : bond 0.00988 ( 3) link_ALPHA1-3 : angle 1.57540 ( 9) link_BETA1-4 : bond 0.00492 ( 30) link_BETA1-4 : angle 1.27267 ( 90) link_NAG-ASN : bond 0.00271 ( 45) link_NAG-ASN : angle 2.50686 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8739 (mt) REVERT: A 151 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8252 (mtt90) REVERT: A 358 ILE cc_start: 0.7586 (mm) cc_final: 0.7283 (mm) REVERT: A 426 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.6775 (tmm) REVERT: B 601 LYS cc_start: 0.8857 (mttp) cc_final: 0.8458 (mtmt) REVERT: C 492 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8360 (mt-10) REVERT: C 500 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7434 (mtm180) REVERT: D 654 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7097 (mt-10) REVERT: E 117 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7973 (mttp) REVERT: G 100 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.6963 (p) REVERT: K 82 MET cc_start: 0.3637 (mmm) cc_final: 0.2058 (ptm) outliers start: 40 outliers final: 30 residues processed: 195 average time/residue: 0.1729 time to fit residues: 49.8496 Evaluate side-chains 198 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 195 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 160 optimal weight: 0.0270 chunk 81 optimal weight: 0.4980 chunk 194 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 616 ASN C 355 ASN E 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.195240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.116775 restraints weight = 20283.195| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.81 r_work: 0.2738 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 20601 Z= 0.095 Angle : 0.528 11.035 28158 Z= 0.261 Chirality : 0.042 0.286 3366 Planarity : 0.004 0.052 3447 Dihedral : 4.648 54.415 4266 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.15 % Favored : 97.77 % Rotamer: Outliers : 1.74 % Allowed : 15.42 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.17), residues: 2373 helix: 1.87 (0.29), residues: 408 sheet: 0.79 (0.18), residues: 777 loop : -0.75 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 444 TYR 0.011 0.001 TYR E 173 PHE 0.015 0.001 PHE E 53 TRP 0.012 0.001 TRP E 427 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00212 (20478) covalent geometry : angle 0.49485 (27831) SS BOND : bond 0.00507 ( 42) SS BOND : angle 1.55979 ( 84) hydrogen bonds : bond 0.03602 ( 739) hydrogen bonds : angle 4.14507 ( 2034) link_ALPHA1-2 : bond 0.00304 ( 3) link_ALPHA1-2 : angle 1.62725 ( 9) link_ALPHA1-3 : bond 0.00858 ( 3) link_ALPHA1-3 : angle 1.44151 ( 9) link_BETA1-4 : bond 0.00491 ( 30) link_BETA1-4 : angle 1.14649 ( 90) link_NAG-ASN : bond 0.00265 ( 45) link_NAG-ASN : angle 2.23954 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5119.60 seconds wall clock time: 88 minutes 26.14 seconds (5306.14 seconds total)