Starting phenix.real_space_refine on Fri Aug 7 00:35:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tl2_41359/08_2026/8tl2_41359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tl2_41359/08_2026/8tl2_41359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tl2_41359/08_2026/8tl2_41359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tl2_41359/08_2026/8tl2_41359.map" model { file = "/net/cci-nas-00/data/ceres_data/8tl2_41359/08_2026/8tl2_41359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tl2_41359/08_2026/8tl2_41359.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 122 5.16 5 C 11463 2.51 5 N 3054 2.21 5 O 3684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18323 Number of models: 1 Model: "" Number of chains: 43 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: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 989 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "H" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 851 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "K" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 989 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "L" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 851 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 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: 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: "k" 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: "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: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.39, per 1000 atoms: 0.24 Number of scatterers: 18323 At special positions: 0 Unit cell: (128.691, 134.737, 158.921, 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 122 16.00 O 3684 8.00 N 3054 7.00 C 11463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 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 K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN Y 4 " - " MAN Y 5 " " MAN k 4 " - " MAN k 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " " BMA k 3 " - " MAN k 4 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG 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 h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 133 " " NAG I 1 " - " ASN A 448 " " NAG J 1 " - " ASN A 160 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 363 " " NAG T 1 " - " ASN C 448 " " NAG U 1 " - " ASN C 160 " " NAG V 1 " - " ASN C 88 " " 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 88 " " NAG i 1 " - " ASN E 276 " " NAG j 1 " - " ASN E 386 " " NAG k 1 " - " ASN E 262 " " NAG l 1 " - " ASN E 156 " " NAG m 1 " - " ASN E 332 " " NAG n 1 " - " ASN E 363 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 837.5 milliseconds 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4066 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 37 sheets defined 20.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.471A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.623A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.222A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.148A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.603A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 663 removed outlier: 3.883A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.609A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 removed outlier: 3.634A pdb=" N ARG C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.877A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.520A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.252A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 4.075A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.647A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 639 through 662 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.547A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 removed outlier: 3.853A pdb=" N ARG E 151 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.605A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 527 removed outlier: 3.736A pdb=" N ALA F 525 " --> pdb=" O PHE F 522 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.180A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.638A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 639 through 662 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.653A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.980A pdb=" N PHE H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.857A pdb=" N PHE L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.389A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.164A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.366A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.494A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.581A pdb=" N PHE A 288 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.798A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.781A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.409A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 516 through 518 removed outlier: 6.499A pdb=" N GLY B 516 " --> pdb=" O GLU G 97 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ARG G 99 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL B 518 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU G 95 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR G 34 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP G 35 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN G 50 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER G 40 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.576A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.798A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.358A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.185A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.479A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.422A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.255A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.902A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 170 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.529A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.471A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.242A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.551A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 516 through 518 removed outlier: 6.419A pdb=" N GLY F 516 " --> pdb=" O GLU K 97 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ARG K 99 " --> pdb=" O GLY F 516 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL F 518 " --> pdb=" O ARG K 99 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU K 95 " --> pdb=" O TYR K 34 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TYR K 34 " --> pdb=" O LEU K 95 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP K 35 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN K 50 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AD3, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.691A pdb=" N ASP H 105 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA H 13 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.691A pdb=" N ASP H 105 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA H 13 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.657A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA L 13 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.657A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA L 13 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.79 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 5806 1.36 - 1.50: 5192 1.50 - 1.64: 7521 1.64 - 1.77: 3 1.77 - 1.91: 161 Bond restraints: 18683 Sorted by residual: bond pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " ideal model delta sigma weight residual 1.808 1.912 -0.104 3.30e-02 9.18e+02 9.94e+00 bond pdb=" CB CYS E 331 " pdb=" SG CYS E 331 " ideal model delta sigma weight residual 1.808 1.910 -0.102 3.30e-02 9.18e+02 9.57e+00 bond pdb=" C ARG C 298 " pdb=" N PRO C 299 " ideal model delta sigma weight residual 1.332 1.359 -0.027 8.90e-03 1.26e+04 8.87e+00 bond pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 1.808 1.711 0.097 3.30e-02 9.18e+02 8.64e+00 bond pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 1.808 1.714 0.094 3.30e-02 9.18e+02 8.18e+00 ... (remaining 18678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 25206 3.57 - 7.13: 163 7.13 - 10.70: 3 10.70 - 14.27: 0 14.27 - 17.83: 2 Bond angle restraints: 25374 Sorted by residual: angle pdb=" CA CYS A 296 " pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 114.40 132.23 -17.83 2.30e+00 1.89e-01 6.01e+01 angle pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 114.40 131.84 -17.44 2.30e+00 1.89e-01 5.75e+01 angle pdb=" C CYS C 218 " pdb=" N ALA C 219 " pdb=" CA ALA C 219 " ideal model delta sigma weight residual 121.48 129.28 -7.80 2.04e+00 2.40e-01 1.46e+01 angle pdb=" N CYS E 296 " pdb=" CA CYS E 296 " pdb=" C CYS E 296 " ideal model delta sigma weight residual 108.79 114.09 -5.30 1.53e+00 4.27e-01 1.20e+01 angle pdb=" CA CYS C 418 " pdb=" CB CYS C 418 " pdb=" SG CYS C 418 " ideal model delta sigma weight residual 114.40 122.19 -7.79 2.30e+00 1.89e-01 1.15e+01 ... (remaining 25369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 11146 21.90 - 43.80: 900 43.80 - 65.70: 182 65.70 - 87.60: 67 87.60 - 109.49: 27 Dihedral angle restraints: 12322 sinusoidal: 6023 harmonic: 6299 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual 93.00 -179.94 -87.06 1 1.00e+01 1.00e-02 9.11e+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 13.33 79.67 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 21.43 71.57 1 1.00e+01 1.00e-02 6.56e+01 ... (remaining 12319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2659 0.062 - 0.125: 392 0.125 - 0.187: 47 0.187 - 0.249: 2 0.249 - 0.311: 9 Chirality restraints: 3109 Sorted by residual: 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 -2.09 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.94e+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 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 3106 not shown) Planarity restraints: 3166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 75 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.08e+00 pdb=" N PRO A 76 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 542 " -0.137 9.50e-02 1.11e+02 6.19e-02 2.82e+00 pdb=" NE ARG D 542 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D 542 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 542 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 542 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 632 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" CG ASP B 632 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP B 632 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP B 632 " -0.010 2.00e-02 2.50e+03 ... (remaining 3163 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 189 2.64 - 3.20: 15205 3.20 - 3.77: 25272 3.77 - 4.33: 35833 4.33 - 4.90: 61440 Nonbonded interactions: 137939 Sorted by model distance: nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.072 3.040 nonbonded pdb=" OG1 THR A 297 " pdb=" O ILE A 443 " model vdw 2.086 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.106 3.040 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.135 3.040 nonbonded pdb=" O ASP H 82 " pdb=" OH TYR H 86 " model vdw 2.153 3.040 ... (remaining 137934 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 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' 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 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' selection = chain 'n' } ncs_group { reference = chain 'M' selection = chain 'V' selection = chain 'h' } ncs_group { reference = chain 'P' selection = chain 'Y' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.060 Find NCS groups from input model: 0.720 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.005 0.104 18810 Z= 0.231 Angle : 0.757 17.831 25715 Z= 0.354 Chirality : 0.048 0.311 3109 Planarity : 0.003 0.062 3121 Dihedral : 16.897 109.495 8136 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.26 % Allowed : 13.76 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2143 helix: 1.86 (0.29), residues: 417 sheet: 0.43 (0.20), residues: 643 loop : -0.75 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 542 TYR 0.012 0.001 TYR L 91 PHE 0.010 0.001 PHE E 383 TRP 0.007 0.001 TRP H 35 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 (18683) covalent geometry : angle 0.72813 / 0.34 (25374) SS BOND : bond 0.00658 / 0.44 ( 40) SS BOND : angle 2.53655 / 1.84 ( 80) hydrogen bonds : bond 0.11175 / 7.69 ( 646) hydrogen bonds : angle 5.05188 / 3.40 ( 1752) link_ALPHA1-2 : bond 0.00267 / 0.12 ( 3) link_ALPHA1-2 : angle 1.77534 / 1.03 ( 9) link_ALPHA1-3 : bond 0.00501 / 0.23 ( 3) link_ALPHA1-3 : angle 1.44343 / 0.85 ( 9) link_BETA1-4 : bond 0.00499 / 0.31 ( 36) link_BETA1-4 : angle 1.03200 / 0.73 ( 108) link_NAG-ASN : bond 0.00297 / 0.19 ( 45) link_NAG-ASN : angle 2.10819 / 1.48 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 185 time to evaluate : 0.628 Fit side-chains REVERT: E 207 LYS cc_start: 0.7927 (mtmm) cc_final: 0.7666 (mmtm) REVERT: E 271 MET cc_start: 0.9005 (mmm) cc_final: 0.8594 (mmt) REVERT: F 543 ASN cc_start: 0.8368 (m-40) cc_final: 0.8168 (m110) outliers start: 5 outliers final: 3 residues processed: 189 average time/residue: 0.1645 time to fit residues: 45.0460 Evaluate side-chains 178 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain K residue 80 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.3114 > 50:) chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 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: 2.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 30.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN C 67 ASN C 462 ASN E 355 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.172107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.117611 restraints weight = 21058.998| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 4.27 r_work: 0.2947 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 18810 Z= 0.274 Angle : 0.809 16.298 25715 Z= 0.391 Chirality : 0.051 0.331 3109 Planarity : 0.005 0.049 3121 Dihedral : 9.979 74.980 4136 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 2.55 % Allowed : 15.02 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 2143 helix: 1.68 (0.29), residues: 402 sheet: 0.11 (0.20), residues: 643 loop : -0.94 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 542 TYR 0.017 0.002 TYR A 384 PHE 0.025 0.003 PHE E 383 TRP 0.012 0.002 TRP C 427 HIS 0.007 0.002 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.27 (18683) covalent geometry : angle 0.76766 / 0.38 (25374) SS BOND : bond 0.00711 / 0.45 ( 40) SS BOND : angle 2.72849 / 1.91 ( 80) hydrogen bonds : bond 0.06417 / 4.29 ( 646) hydrogen bonds : angle 4.77524 / 3.25 ( 1752) link_ALPHA1-2 : bond 0.00697 / 0.34 ( 3) link_ALPHA1-2 : angle 2.08039 / 1.23 ( 9) link_ALPHA1-3 : bond 0.01441 / 0.65 ( 3) link_ALPHA1-3 : angle 2.03876 / 1.31 ( 9) link_BETA1-4 : bond 0.00806 / 0.51 ( 36) link_BETA1-4 : angle 1.56171 / 1.17 ( 108) link_NAG-ASN : bond 0.00456 / 0.30 ( 45) link_NAG-ASN : angle 2.62125 / 1.85 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: B 655 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6847 (ptpt) REVERT: C 426 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7517 (tpt) REVERT: E 54 CYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7219 (t) REVERT: E 136 ASN cc_start: 0.6517 (m-40) cc_final: 0.5911 (p0) REVERT: G 107 LEU cc_start: 0.5605 (mt) cc_final: 0.5359 (mt) outliers start: 49 outliers final: 23 residues processed: 231 average time/residue: 0.1494 time to fit residues: 51.3812 Evaluate side-chains 209 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 355 ASN B 607 ASN E 137 ASN G 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.174304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119549 restraints weight = 21060.780| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 4.22 r_work: 0.2934 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 18810 Z= 0.161 Angle : 0.648 14.416 25715 Z= 0.315 Chirality : 0.045 0.300 3109 Planarity : 0.004 0.046 3121 Dihedral : 7.922 56.327 4136 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.11 % Rotamer: Outliers : 2.92 % Allowed : 15.59 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.18), residues: 2143 helix: 1.77 (0.29), residues: 402 sheet: 0.24 (0.20), residues: 630 loop : -0.96 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 542 TYR 0.011 0.001 TYR H 49 PHE 0.020 0.002 PHE E 383 TRP 0.011 0.001 TRP C 427 HIS 0.004 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.16 (18683) covalent geometry : angle 0.60459 / 0.30 (25374) SS BOND : bond 0.00521 / 0.34 ( 40) SS BOND : angle 2.38000 / 1.65 ( 80) hydrogen bonds : bond 0.04767 / 3.23 ( 646) hydrogen bonds : angle 4.46968 / 3.05 ( 1752) link_ALPHA1-2 : bond 0.00393 / 0.19 ( 3) link_ALPHA1-2 : angle 1.69546 / 1.01 ( 9) link_ALPHA1-3 : bond 0.01398 / 0.63 ( 3) link_ALPHA1-3 : angle 1.53079 / 1.00 ( 9) link_BETA1-4 : bond 0.00589 / 0.38 ( 36) link_BETA1-4 : angle 1.36864 / 1.02 ( 108) link_NAG-ASN : bond 0.00271 / 0.17 ( 45) link_NAG-ASN : angle 2.45936 / 1.77 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8452 (mpt-90) REVERT: B 655 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6838 (ptpt) REVERT: E 446 VAL cc_start: 0.9100 (m) cc_final: 0.8883 (t) REVERT: G 107 LEU cc_start: 0.5650 (mt) cc_final: 0.5385 (mt) REVERT: K 94 THR cc_start: 0.8475 (t) cc_final: 0.7990 (m) outliers start: 56 outliers final: 34 residues processed: 233 average time/residue: 0.1518 time to fit residues: 52.4459 Evaluate side-chains 222 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 80 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 99 optimal weight: 0.3980 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 178 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.173876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119228 restraints weight = 21192.881| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.31 r_work: 0.2939 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18810 Z= 0.159 Angle : 0.639 11.166 25715 Z= 0.311 Chirality : 0.045 0.310 3109 Planarity : 0.004 0.048 3121 Dihedral : 6.839 49.834 4136 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 3.44 % Allowed : 15.85 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.18), residues: 2143 helix: 1.75 (0.29), residues: 402 sheet: 0.23 (0.20), residues: 633 loop : -0.97 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 500 TYR 0.011 0.001 TYR H 49 PHE 0.020 0.002 PHE E 383 TRP 0.011 0.001 TRP C 427 HIS 0.004 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (18683) covalent geometry : angle 0.59685 / 0.30 (25374) SS BOND : bond 0.00510 / 0.33 ( 40) SS BOND : angle 2.27485 / 1.57 ( 80) hydrogen bonds : bond 0.04766 / 3.23 ( 646) hydrogen bonds : angle 4.43150 / 3.03 ( 1752) link_ALPHA1-2 : bond 0.00348 / 0.17 ( 3) link_ALPHA1-2 : angle 1.65653 / 0.97 ( 9) link_ALPHA1-3 : bond 0.01302 / 0.58 ( 3) link_ALPHA1-3 : angle 1.55746 / 1.02 ( 9) link_BETA1-4 : bond 0.00591 / 0.38 ( 36) link_BETA1-4 : angle 1.36437 / 1.01 ( 108) link_NAG-ASN : bond 0.00247 / 0.16 ( 45) link_NAG-ASN : angle 2.43032 / 1.75 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 182 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: B 655 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6838 (ptpt) REVERT: C 69 TRP cc_start: 0.7022 (OUTLIER) cc_final: 0.6525 (m100) REVERT: C 351 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7752 (mttp) REVERT: E 54 CYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6879 (t) REVERT: G 107 LEU cc_start: 0.5668 (mt) cc_final: 0.5400 (mt) REVERT: K 94 THR cc_start: 0.8487 (t) cc_final: 0.8035 (m) outliers start: 66 outliers final: 47 residues processed: 237 average time/residue: 0.1492 time to fit residues: 52.7647 Evaluate side-chains 231 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 80 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 81 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN E 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.174643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120390 restraints weight = 21011.016| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 4.10 r_work: 0.2985 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 18810 Z= 0.134 Angle : 0.610 13.885 25715 Z= 0.297 Chirality : 0.044 0.306 3109 Planarity : 0.003 0.045 3121 Dihedral : 5.950 50.393 4136 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 3.18 % Allowed : 16.21 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.18), residues: 2143 helix: 1.82 (0.29), residues: 402 sheet: 0.31 (0.20), residues: 630 loop : -0.93 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 542 TYR 0.011 0.001 TYR H 49 PHE 0.018 0.001 PHE E 383 TRP 0.010 0.001 TRP C 427 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.13 (18683) covalent geometry : angle 0.56620 / 0.28 (25374) SS BOND : bond 0.00592 / 0.40 ( 40) SS BOND : angle 2.30095 / 1.59 ( 80) hydrogen bonds : bond 0.04336 / 2.94 ( 646) hydrogen bonds : angle 4.32377 / 2.95 ( 1752) link_ALPHA1-2 : bond 0.00318 / 0.15 ( 3) link_ALPHA1-2 : angle 1.65904 / 0.97 ( 9) link_ALPHA1-3 : bond 0.01255 / 0.56 ( 3) link_ALPHA1-3 : angle 1.53939 / 1.01 ( 9) link_BETA1-4 : bond 0.00558 / 0.36 ( 36) link_BETA1-4 : angle 1.27037 / 0.92 ( 108) link_NAG-ASN : bond 0.00273 / 0.17 ( 45) link_NAG-ASN : angle 2.41632 / 1.74 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 192 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8294 (tttp) cc_final: 0.8086 (ttpp) REVERT: B 655 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6815 (ptpt) REVERT: C 54 CYS cc_start: 0.7836 (t) cc_final: 0.7508 (t) REVERT: C 69 TRP cc_start: 0.6951 (OUTLIER) cc_final: 0.6346 (m100) REVERT: C 351 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7717 (mttp) REVERT: E 232 LYS cc_start: 0.8673 (mttp) cc_final: 0.8315 (mmtm) REVERT: G 107 LEU cc_start: 0.5632 (mt) cc_final: 0.5366 (mt) REVERT: H 90 GLN cc_start: 0.6793 (pp30) cc_final: 0.5849 (pp30) REVERT: K 94 THR cc_start: 0.8508 (t) cc_final: 0.8075 (m) outliers start: 61 outliers final: 45 residues processed: 243 average time/residue: 0.1483 time to fit residues: 53.4576 Evaluate side-chains 237 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 80 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN E 355 ASN H 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.174227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119094 restraints weight = 20885.213| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 4.12 r_work: 0.2924 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18810 Z= 0.144 Angle : 0.618 11.620 25715 Z= 0.301 Chirality : 0.044 0.308 3109 Planarity : 0.004 0.045 3121 Dihedral : 5.529 51.112 4136 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 3.55 % Allowed : 16.74 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.18), residues: 2143 helix: 1.79 (0.29), residues: 402 sheet: 0.34 (0.20), residues: 633 loop : -0.95 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 542 TYR 0.010 0.001 TYR H 49 PHE 0.023 0.002 PHE C 53 TRP 0.011 0.001 TRP C 427 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.14 (18683) covalent geometry : angle 0.57348 / 0.29 (25374) SS BOND : bond 0.00493 / 0.32 ( 40) SS BOND : angle 2.47286 / 1.73 ( 80) hydrogen bonds : bond 0.04466 / 3.03 ( 646) hydrogen bonds : angle 4.31071 / 2.94 ( 1752) link_ALPHA1-2 : bond 0.00314 / 0.16 ( 3) link_ALPHA1-2 : angle 1.69048 / 1.00 ( 9) link_ALPHA1-3 : bond 0.01253 / 0.55 ( 3) link_ALPHA1-3 : angle 1.42948 / 0.93 ( 9) link_BETA1-4 : bond 0.00552 / 0.36 ( 36) link_BETA1-4 : angle 1.25633 / 0.90 ( 108) link_NAG-ASN : bond 0.00252 / 0.17 ( 45) link_NAG-ASN : angle 2.37193 / 1.71 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 189 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8469 (tttp) cc_final: 0.8251 (ttpp) REVERT: B 621 GLU cc_start: 0.7699 (mm-30) cc_final: 0.6641 (tm-30) REVERT: B 655 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6790 (ptpt) REVERT: C 54 CYS cc_start: 0.8174 (t) cc_final: 0.7838 (t) REVERT: C 69 TRP cc_start: 0.6946 (OUTLIER) cc_final: 0.6353 (m100) REVERT: E 54 CYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7272 (t) REVERT: E 232 LYS cc_start: 0.8701 (mttp) cc_final: 0.8324 (mmtm) REVERT: G 107 LEU cc_start: 0.5637 (mt) cc_final: 0.5361 (mt) REVERT: H 90 GLN cc_start: 0.6920 (pp30) cc_final: 0.5927 (pp30) REVERT: K 94 THR cc_start: 0.8677 (t) cc_final: 0.8266 (m) REVERT: L 4 MET cc_start: 0.5580 (tpt) cc_final: 0.5279 (tpt) outliers start: 68 outliers final: 51 residues processed: 246 average time/residue: 0.1475 time to fit residues: 53.8742 Evaluate side-chains 239 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 80 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 17 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 110 optimal weight: 0.3980 chunk 157 optimal weight: 0.6980 chunk 176 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN A 462 ASN C 67 ASN E 137 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 = 0.3927 r_free = 0.3927 target = 0.172379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116914 restraints weight = 21007.502| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.12 r_work: 0.2972 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 18810 Z= 0.195 Angle : 0.686 15.035 25715 Z= 0.332 Chirality : 0.046 0.326 3109 Planarity : 0.004 0.046 3121 Dihedral : 5.522 51.695 4136 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 3.81 % Allowed : 16.68 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.18), residues: 2143 helix: 1.66 (0.29), residues: 402 sheet: 0.25 (0.20), residues: 641 loop : -1.02 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 542 TYR 0.013 0.001 TYR A 384 PHE 0.022 0.002 PHE E 383 TRP 0.010 0.001 TRP A 427 HIS 0.005 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.19 (18683) covalent geometry : angle 0.64251 / 0.32 (25374) SS BOND : bond 0.00583 / 0.38 ( 40) SS BOND : angle 2.60329 / 1.81 ( 80) hydrogen bonds : bond 0.05229 / 3.53 ( 646) hydrogen bonds : angle 4.42827 / 3.03 ( 1752) link_ALPHA1-2 : bond 0.00334 / 0.17 ( 3) link_ALPHA1-2 : angle 1.70859 / 1.01 ( 9) link_ALPHA1-3 : bond 0.01194 / 0.53 ( 3) link_ALPHA1-3 : angle 1.29677 / 0.84 ( 9) link_BETA1-4 : bond 0.00573 / 0.37 ( 36) link_BETA1-4 : angle 1.26703 / 0.90 ( 108) link_NAG-ASN : bond 0.00308 / 0.20 ( 45) link_NAG-ASN : angle 2.52765 / 1.81 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 190 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8461 (tttp) cc_final: 0.8236 (ttpp) REVERT: B 621 GLU cc_start: 0.7715 (mm-30) cc_final: 0.6635 (tm-30) REVERT: B 655 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6771 (ptpt) REVERT: C 54 CYS cc_start: 0.8264 (t) cc_final: 0.7903 (t) REVERT: C 69 TRP cc_start: 0.6973 (OUTLIER) cc_final: 0.6549 (m100) REVERT: E 54 CYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7112 (t) REVERT: E 136 ASN cc_start: 0.6613 (m-40) cc_final: 0.5935 (p0) REVERT: E 232 LYS cc_start: 0.8728 (mttp) cc_final: 0.8331 (mmtm) REVERT: G 107 LEU cc_start: 0.5646 (mt) cc_final: 0.5382 (mt) REVERT: H 90 GLN cc_start: 0.6916 (pp30) cc_final: 0.5964 (pp30) REVERT: K 94 THR cc_start: 0.8718 (t) cc_final: 0.8316 (m) REVERT: L 4 MET cc_start: 0.5536 (tpt) cc_final: 0.5312 (mmm) outliers start: 73 outliers final: 56 residues processed: 252 average time/residue: 0.1450 time to fit residues: 54.8341 Evaluate side-chains 247 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 188 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 80 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 105 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 20 optimal weight: 0.0040 chunk 141 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN E 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.174874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.120106 restraints weight = 20921.079| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.20 r_work: 0.2961 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 18810 Z= 0.120 Angle : 0.601 14.588 25715 Z= 0.294 Chirality : 0.043 0.305 3109 Planarity : 0.003 0.044 3121 Dihedral : 5.129 52.074 4136 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 3.08 % Allowed : 17.52 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2143 helix: 1.79 (0.29), residues: 402 sheet: 0.37 (0.20), residues: 650 loop : -0.94 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 542 TYR 0.011 0.001 TYR G 102 PHE 0.018 0.001 PHE E 383 TRP 0.012 0.001 TRP C 427 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (18683) covalent geometry : angle 0.55685 / 0.28 (25374) SS BOND : bond 0.00585 / 0.39 ( 40) SS BOND : angle 2.41896 / 1.68 ( 80) hydrogen bonds : bond 0.04075 / 2.78 ( 646) hydrogen bonds : angle 4.23053 / 2.89 ( 1752) link_ALPHA1-2 : bond 0.00256 / 0.13 ( 3) link_ALPHA1-2 : angle 1.69973 / 1.00 ( 9) link_ALPHA1-3 : bond 0.01084 / 0.48 ( 3) link_ALPHA1-3 : angle 1.21801 / 0.79 ( 9) link_BETA1-4 : bond 0.00520 / 0.33 ( 36) link_BETA1-4 : angle 1.16095 / 0.84 ( 108) link_NAG-ASN : bond 0.00274 / 0.18 ( 45) link_NAG-ASN : angle 2.38275 / 1.72 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8628 (mm) REVERT: A 347 LYS cc_start: 0.8324 (tttp) cc_final: 0.8122 (ttpp) REVERT: B 621 GLU cc_start: 0.7618 (mm-30) cc_final: 0.6655 (tm-30) REVERT: B 655 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6844 (ptpt) REVERT: C 54 CYS cc_start: 0.7907 (t) cc_final: 0.7557 (t) REVERT: C 69 TRP cc_start: 0.6949 (OUTLIER) cc_final: 0.6234 (m100) REVERT: E 54 CYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6889 (t) REVERT: E 232 LYS cc_start: 0.8672 (mttp) cc_final: 0.8331 (mmtm) REVERT: E 325 ASP cc_start: 0.8211 (t0) cc_final: 0.7886 (t0) REVERT: G 107 LEU cc_start: 0.5631 (mt) cc_final: 0.5373 (mt) REVERT: H 45 GLN cc_start: 0.6767 (tt0) cc_final: 0.6563 (mt0) REVERT: H 90 GLN cc_start: 0.6764 (pp30) cc_final: 0.5890 (pp30) REVERT: K 76 ASN cc_start: 0.5974 (OUTLIER) cc_final: 0.5580 (m110) REVERT: K 94 THR cc_start: 0.8610 (t) cc_final: 0.8212 (m) outliers start: 59 outliers final: 48 residues processed: 239 average time/residue: 0.1467 time to fit residues: 52.3421 Evaluate side-chains 238 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 185 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 80 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 122 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 0.0770 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN E 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.175063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120641 restraints weight = 20850.897| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.83 r_work: 0.3026 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18810 Z= 0.123 Angle : 0.599 14.374 25715 Z= 0.292 Chirality : 0.043 0.305 3109 Planarity : 0.003 0.044 3121 Dihedral : 4.929 52.819 4136 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.97 % Rotamer: Outliers : 2.87 % Allowed : 17.67 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2143 helix: 1.85 (0.29), residues: 402 sheet: 0.39 (0.20), residues: 652 loop : -0.91 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 542 TYR 0.011 0.001 TYR H 49 PHE 0.018 0.001 PHE E 383 TRP 0.010 0.001 TRP C 427 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 (18683) covalent geometry : angle 0.55728 / 0.28 (25374) SS BOND : bond 0.00520 / 0.35 ( 40) SS BOND : angle 2.38193 / 1.64 ( 80) hydrogen bonds : bond 0.04084 / 2.78 ( 646) hydrogen bonds : angle 4.18945 / 2.86 ( 1752) link_ALPHA1-2 : bond 0.00297 / 0.15 ( 3) link_ALPHA1-2 : angle 1.64342 / 0.97 ( 9) link_ALPHA1-3 : bond 0.01029 / 0.46 ( 3) link_ALPHA1-3 : angle 1.12870 / 0.72 ( 9) link_BETA1-4 : bond 0.00519 / 0.33 ( 36) link_BETA1-4 : angle 1.14209 / 0.82 ( 108) link_NAG-ASN : bond 0.00262 / 0.18 ( 45) link_NAG-ASN : angle 2.31724 / 1.66 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.7985 (tp40) cc_final: 0.7187 (tt0) REVERT: A 125 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8687 (mm) REVERT: A 347 LYS cc_start: 0.8473 (tttp) cc_final: 0.8259 (ttpp) REVERT: B 621 GLU cc_start: 0.7738 (mm-30) cc_final: 0.6695 (tm-30) REVERT: B 655 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6907 (ptpt) REVERT: C 69 TRP cc_start: 0.7038 (OUTLIER) cc_final: 0.6421 (m100) REVERT: E 232 LYS cc_start: 0.8701 (mttp) cc_final: 0.8330 (mmtm) REVERT: E 325 ASP cc_start: 0.8329 (t0) cc_final: 0.8007 (t0) REVERT: G 107 LEU cc_start: 0.5525 (mt) cc_final: 0.5239 (mt) REVERT: H 45 GLN cc_start: 0.6847 (tt0) cc_final: 0.6607 (mt0) REVERT: H 90 GLN cc_start: 0.7060 (pp30) cc_final: 0.6187 (pp30) REVERT: K 76 ASN cc_start: 0.6004 (OUTLIER) cc_final: 0.5552 (m110) REVERT: K 94 THR cc_start: 0.8772 (t) cc_final: 0.8410 (m) outliers start: 55 outliers final: 46 residues processed: 233 average time/residue: 0.1499 time to fit residues: 52.1501 Evaluate side-chains 234 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 chunk 126 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN E 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.174903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.119965 restraints weight = 20864.540| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 4.17 r_work: 0.2969 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18810 Z= 0.131 Angle : 0.608 14.293 25715 Z= 0.296 Chirality : 0.043 0.305 3109 Planarity : 0.003 0.044 3121 Dihedral : 4.883 52.841 4135 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 2.92 % Allowed : 17.88 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2143 helix: 1.83 (0.29), residues: 402 sheet: 0.39 (0.20), residues: 652 loop : -0.92 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 178 TYR 0.010 0.001 TYR H 49 PHE 0.018 0.001 PHE E 383 TRP 0.010 0.001 TRP C 427 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (18683) covalent geometry : angle 0.56699 / 0.28 (25374) SS BOND : bond 0.00565 / 0.36 ( 40) SS BOND : angle 2.40258 / 1.64 ( 80) hydrogen bonds : bond 0.04144 / 2.82 ( 646) hydrogen bonds : angle 4.19961 / 2.87 ( 1752) link_ALPHA1-2 : bond 0.00307 / 0.15 ( 3) link_ALPHA1-2 : angle 1.62764 / 0.96 ( 9) link_ALPHA1-3 : bond 0.00985 / 0.44 ( 3) link_ALPHA1-3 : angle 1.09021 / 0.69 ( 9) link_BETA1-4 : bond 0.00529 / 0.34 ( 36) link_BETA1-4 : angle 1.13037 / 0.81 ( 108) link_NAG-ASN : bond 0.00254 / 0.17 ( 45) link_NAG-ASN : angle 2.31155 / 1.66 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 114 GLN cc_start: 0.7816 (tp40) cc_final: 0.7069 (tt0) REVERT: A 125 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8621 (mm) REVERT: A 347 LYS cc_start: 0.8312 (tttp) cc_final: 0.8099 (ttpp) REVERT: B 621 GLU cc_start: 0.7625 (mm-30) cc_final: 0.6666 (tm-30) REVERT: B 655 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6822 (ptpt) REVERT: C 69 TRP cc_start: 0.6920 (OUTLIER) cc_final: 0.6297 (m100) REVERT: E 232 LYS cc_start: 0.8672 (mttp) cc_final: 0.8299 (mmtm) REVERT: E 325 ASP cc_start: 0.8204 (t0) cc_final: 0.7882 (t0) REVERT: G 107 LEU cc_start: 0.5533 (mt) cc_final: 0.5256 (mt) REVERT: H 90 GLN cc_start: 0.6813 (pp30) cc_final: 0.5957 (pp30) REVERT: K 76 ASN cc_start: 0.5851 (OUTLIER) cc_final: 0.5444 (m110) REVERT: K 94 THR cc_start: 0.8598 (t) cc_final: 0.8220 (m) outliers start: 56 outliers final: 50 residues processed: 228 average time/residue: 0.1458 time to fit residues: 49.5028 Evaluate side-chains 236 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 357 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 130 optimal weight: 0.0270 chunk 201 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN E 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.175058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120363 restraints weight = 20920.328| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.01 r_work: 0.2974 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18810 Z= 0.131 Angle : 0.608 14.863 25715 Z= 0.296 Chirality : 0.043 0.303 3109 Planarity : 0.003 0.044 3121 Dihedral : 4.797 52.901 4135 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 2.92 % Allowed : 17.94 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.18), residues: 2143 helix: 1.84 (0.29), residues: 402 sheet: 0.40 (0.20), residues: 652 loop : -0.91 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 542 TYR 0.011 0.001 TYR G 102 PHE 0.018 0.001 PHE E 383 TRP 0.010 0.001 TRP C 427 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 (18683) covalent geometry : angle 0.56746 / 0.28 (25374) SS BOND : bond 0.00562 / 0.37 ( 40) SS BOND : angle 2.37212 / 1.61 ( 80) hydrogen bonds : bond 0.04151 / 2.82 ( 646) hydrogen bonds : angle 4.20257 / 2.87 ( 1752) link_ALPHA1-2 : bond 0.00321 / 0.15 ( 3) link_ALPHA1-2 : angle 1.61326 / 0.94 ( 9) link_ALPHA1-3 : bond 0.00916 / 0.41 ( 3) link_ALPHA1-3 : angle 1.06128 / 0.66 ( 9) link_BETA1-4 : bond 0.00518 / 0.33 ( 36) link_BETA1-4 : angle 1.13404 / 0.81 ( 108) link_NAG-ASN : bond 0.00280 / 0.20 ( 45) link_NAG-ASN : angle 2.31198 / 1.66 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4568.08 seconds wall clock time: 79 minutes 8.41 seconds (4748.41 seconds total)