Starting phenix.real_space_refine on Mon Jun 16 06:39:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tl2_41359/06_2025/8tl2_41359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tl2_41359/06_2025/8tl2_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_41359/06_2025/8tl2_41359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tl2_41359/06_2025/8tl2_41359.map" model { file = "/net/cci-nas-00/data/ceres_data/8tl2_41359/06_2025/8tl2_41359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tl2_41359/06_2025/8tl2_41359.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.30, per 1000 atoms: 0.67 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: 5.80 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.55 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: 6.47 Time building geometry restraints manager: 6.37 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: 0.00 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: 5.620 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: 0.010 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 45.170 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:3.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP H 35 HIS 0.005 0.001 HIS A 216 PHE 0.010 0.001 PHE E 383 TYR 0.012 0.001 TYR L 91 ARG 0.012 0.001 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 45) link_NAG-ASN : angle 2.10819 ( 135) link_BETA1-4 : bond 0.00499 ( 36) link_BETA1-4 : angle 1.03200 ( 108) link_ALPHA1-2 : bond 0.00267 ( 3) link_ALPHA1-2 : angle 1.77534 ( 9) link_ALPHA1-3 : bond 0.00501 ( 3) link_ALPHA1-3 : angle 1.44343 ( 9) hydrogen bonds : bond 0.11175 ( 646) hydrogen bonds : angle 5.05188 ( 1752) SS BOND : bond 0.00658 ( 40) SS BOND : angle 2.53655 ( 80) covalent geometry : bond 0.00488 (18683) covalent geometry : angle 0.72813 (25374) *********************** 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 : 2.053 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: 0.3783 time to fit residues: 102.6211 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 : 1.997 ------------------------------------------------------------------------------- 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 183 optimal weight: 20.0000 chunk 164 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 67 ASN C 80 ASN C 462 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 = 0.3941 r_free = 0.3941 target = 0.173631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118933 restraints weight = 21054.649| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 4.68 r_work: 0.2967 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 18810 Z= 0.233 Angle : 0.756 15.912 25715 Z= 0.365 Chirality : 0.048 0.316 3109 Planarity : 0.004 0.049 3121 Dihedral : 9.874 74.215 4136 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 2.24 % Allowed : 14.91 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2143 helix: 1.71 (0.29), residues: 414 sheet: 0.16 (0.20), residues: 649 loop : -0.87 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 96 HIS 0.006 0.001 HIS E 85 PHE 0.022 0.002 PHE C 383 TYR 0.014 0.002 TYR A 384 ARG 0.007 0.001 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 45) link_NAG-ASN : angle 2.52863 ( 135) link_BETA1-4 : bond 0.00739 ( 36) link_BETA1-4 : angle 1.51556 ( 108) link_ALPHA1-2 : bond 0.00632 ( 3) link_ALPHA1-2 : angle 1.93496 ( 9) link_ALPHA1-3 : bond 0.01385 ( 3) link_ALPHA1-3 : angle 1.99113 ( 9) hydrogen bonds : bond 0.05804 ( 646) hydrogen bonds : angle 4.67146 ( 1752) SS BOND : bond 0.00630 ( 40) SS BOND : angle 2.51933 ( 80) covalent geometry : bond 0.00590 (18683) covalent geometry : angle 0.71576 (25374) *********************** 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 234 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 2.007 Fit side-chains revert: symmetry clash REVERT: B 655 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6740 (ptpt) REVERT: C 117 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7935 (mmtm) REVERT: E 54 CYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7111 (t) REVERT: E 271 MET cc_start: 0.9085 (mmm) cc_final: 0.8675 (mmt) REVERT: E 446 VAL cc_start: 0.9186 (m) cc_final: 0.8981 (t) REVERT: G 107 LEU cc_start: 0.5560 (mt) cc_final: 0.5265 (mt) outliers start: 43 outliers final: 21 residues processed: 225 average time/residue: 0.3485 time to fit residues: 116.7345 Evaluate side-chains 207 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 54 CYS 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 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 80 LEU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 81 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3966 r_free = 0.3966 target = 0.175852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120815 restraints weight = 20889.231| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 4.12 r_work: 0.2975 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18810 Z= 0.135 Angle : 0.615 14.689 25715 Z= 0.299 Chirality : 0.044 0.293 3109 Planarity : 0.003 0.051 3121 Dihedral : 7.791 58.104 4136 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.43 % Rotamer: Outliers : 2.55 % Allowed : 15.80 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2143 helix: 1.89 (0.29), residues: 402 sheet: 0.28 (0.20), residues: 630 loop : -0.89 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 427 HIS 0.003 0.001 HIS A 216 PHE 0.017 0.001 PHE E 383 TYR 0.011 0.001 TYR H 49 ARG 0.007 0.000 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 45) link_NAG-ASN : angle 2.37440 ( 135) link_BETA1-4 : bond 0.00573 ( 36) link_BETA1-4 : angle 1.33752 ( 108) link_ALPHA1-2 : bond 0.00372 ( 3) link_ALPHA1-2 : angle 1.61253 ( 9) link_ALPHA1-3 : bond 0.01326 ( 3) link_ALPHA1-3 : angle 1.46230 ( 9) hydrogen bonds : bond 0.04341 ( 646) hydrogen bonds : angle 4.37261 ( 1752) SS BOND : bond 0.00618 ( 40) SS BOND : angle 2.19553 ( 80) covalent geometry : bond 0.00329 (18683) covalent geometry : angle 0.57376 (25374) *********************** 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 235 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 2.000 Fit side-chains revert: symmetry clash REVERT: B 655 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6807 (ptpt) REVERT: G 107 LEU cc_start: 0.5589 (mt) cc_final: 0.5313 (mt) REVERT: K 94 THR cc_start: 0.8454 (t) cc_final: 0.7966 (m) outliers start: 49 outliers final: 30 residues processed: 223 average time/residue: 0.3428 time to fit residues: 112.2698 Evaluate side-chains 214 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 377 ASN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 413 SER 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 54 CYS 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 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 213 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain F residue 522 PHE 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 Chi-restraints excluded: chain K residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 30 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.171301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116509 restraints weight = 20906.401| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 4.03 r_work: 0.2892 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 18810 Z= 0.260 Angle : 0.744 12.065 25715 Z= 0.361 Chirality : 0.048 0.331 3109 Planarity : 0.004 0.048 3121 Dihedral : 7.021 51.471 4136 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 3.96 % Allowed : 15.07 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2143 helix: 1.56 (0.29), residues: 402 sheet: 0.20 (0.20), residues: 633 loop : -1.02 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 427 HIS 0.006 0.001 HIS E 85 PHE 0.026 0.002 PHE E 383 TYR 0.016 0.002 TYR A 384 ARG 0.004 0.000 ARG E 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 45) link_NAG-ASN : angle 2.59554 ( 135) link_BETA1-4 : bond 0.00661 ( 36) link_BETA1-4 : angle 1.46387 ( 108) link_ALPHA1-2 : bond 0.00404 ( 3) link_ALPHA1-2 : angle 1.68814 ( 9) link_ALPHA1-3 : bond 0.01352 ( 3) link_ALPHA1-3 : angle 1.46215 ( 9) hydrogen bonds : bond 0.05973 ( 646) hydrogen bonds : angle 4.61087 ( 1752) SS BOND : bond 0.00613 ( 40) SS BOND : angle 2.70158 ( 80) covalent geometry : bond 0.00663 (18683) covalent geometry : angle 0.70096 (25374) *********************** 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 268 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 192 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 655 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.6896 (ptpt) REVERT: C 69 TRP cc_start: 0.6971 (OUTLIER) cc_final: 0.6642 (m100) REVERT: C 351 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7843 (mttp) REVERT: E 136 ASN cc_start: 0.6646 (m-40) cc_final: 0.6056 (p0) REVERT: G 107 LEU cc_start: 0.5668 (mt) cc_final: 0.5403 (mt) REVERT: K 94 THR cc_start: 0.8564 (t) cc_final: 0.8132 (m) outliers start: 76 outliers final: 53 residues processed: 250 average time/residue: 0.3216 time to fit residues: 119.8385 Evaluate side-chains 242 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 2.222 ------------------------------------------------------------------------------- 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 182 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 457 ASP Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS 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 244 THR 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 613 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 639 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 365 SER Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 539 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 79 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 94 THR 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 Chi-restraints excluded: chain K residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 152 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 246 GLN E 137 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 = 0.3949 r_free = 0.3949 target = 0.174311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.120000 restraints weight = 21159.697| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 4.56 r_work: 0.2907 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 18810 Z= 0.135 Angle : 0.619 14.309 25715 Z= 0.302 Chirality : 0.044 0.306 3109 Planarity : 0.004 0.045 3121 Dihedral : 6.027 50.409 4136 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.57 % Favored : 97.39 % Rotamer: Outliers : 3.02 % Allowed : 16.89 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2143 helix: 1.72 (0.29), residues: 402 sheet: 0.27 (0.20), residues: 633 loop : -0.95 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 427 HIS 0.003 0.001 HIS A 216 PHE 0.018 0.001 PHE E 383 TYR 0.012 0.001 TYR G 102 ARG 0.007 0.000 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 45) link_NAG-ASN : angle 2.47178 ( 135) link_BETA1-4 : bond 0.00557 ( 36) link_BETA1-4 : angle 1.27286 ( 108) link_ALPHA1-2 : bond 0.00288 ( 3) link_ALPHA1-2 : angle 1.71114 ( 9) link_ALPHA1-3 : bond 0.01265 ( 3) link_ALPHA1-3 : angle 1.58825 ( 9) hydrogen bonds : bond 0.04428 ( 646) hydrogen bonds : angle 4.36441 ( 1752) SS BOND : bond 0.00550 ( 40) SS BOND : angle 2.38955 ( 80) covalent geometry : bond 0.00331 (18683) covalent geometry : angle 0.57382 (25374) *********************** 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: 58 poor density : 195 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8291 (tttp) cc_final: 0.8088 (ttpp) REVERT: B 655 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6694 (ptpt) REVERT: C 69 TRP cc_start: 0.6902 (OUTLIER) cc_final: 0.6195 (m100) REVERT: C 351 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7730 (mttp) REVERT: E 232 LYS cc_start: 0.8625 (mttp) cc_final: 0.8257 (mmtm) REVERT: G 107 LEU cc_start: 0.5524 (mt) cc_final: 0.5261 (mt) REVERT: H 90 GLN cc_start: 0.6619 (pp30) cc_final: 0.5641 (pp30) REVERT: K 94 THR cc_start: 0.8406 (t) cc_final: 0.7967 (m) outliers start: 58 outliers final: 38 residues processed: 243 average time/residue: 0.3415 time to fit residues: 121.5368 Evaluate side-chains 235 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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 377 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 457 ASP 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 54 CYS Chi-restraints excluded: chain C residue 69 TRP 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 396 ILE 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 42 VAL 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 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 413 SER Chi-restraints excluded: chain F residue 522 PHE 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 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 Chi-restraints excluded: chain K residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 1 optimal weight: 0.0670 chunk 186 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 30 optimal weight: 0.0060 chunk 136 optimal weight: 0.9980 overall best weight: 1.2138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 67 ASN E 355 ASN H 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.172825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118363 restraints weight = 21072.407| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 4.20 r_work: 0.2932 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 18810 Z= 0.176 Angle : 0.660 12.645 25715 Z= 0.321 Chirality : 0.045 0.319 3109 Planarity : 0.004 0.049 3121 Dihedral : 5.711 51.292 4136 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 3.55 % Allowed : 16.89 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2143 helix: 1.66 (0.29), residues: 402 sheet: 0.22 (0.20), residues: 639 loop : -0.98 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 427 HIS 0.005 0.001 HIS E 85 PHE 0.020 0.002 PHE E 383 TYR 0.011 0.001 TYR A 384 ARG 0.005 0.000 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 45) link_NAG-ASN : angle 2.46705 ( 135) link_BETA1-4 : bond 0.00574 ( 36) link_BETA1-4 : angle 1.26943 ( 108) link_ALPHA1-2 : bond 0.00321 ( 3) link_ALPHA1-2 : angle 1.73024 ( 9) link_ALPHA1-3 : bond 0.01227 ( 3) link_ALPHA1-3 : angle 1.40462 ( 9) hydrogen bonds : bond 0.05023 ( 646) hydrogen bonds : angle 4.40254 ( 1752) SS BOND : bond 0.00571 ( 40) SS BOND : angle 2.50697 ( 80) covalent geometry : bond 0.00445 (18683) covalent geometry : angle 0.61743 (25374) *********************** 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 256 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 188 time to evaluate : 2.091 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8331 (tttp) cc_final: 0.8117 (ttpp) REVERT: B 655 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6722 (ptpt) REVERT: C 69 TRP cc_start: 0.6953 (OUTLIER) cc_final: 0.6450 (m100) REVERT: C 161 MET cc_start: 0.9103 (tpt) cc_final: 0.8833 (mmm) REVERT: C 351 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7775 (mttp) REVERT: E 136 ASN cc_start: 0.6568 (m-40) cc_final: 0.5981 (p0) REVERT: E 232 LYS cc_start: 0.8629 (mttp) cc_final: 0.8228 (mmtm) REVERT: G 107 LEU cc_start: 0.5611 (mt) cc_final: 0.5341 (mt) REVERT: H 90 GLN cc_start: 0.6691 (pp30) cc_final: 0.5731 (pp30) REVERT: K 94 THR cc_start: 0.8554 (t) cc_final: 0.8126 (m) outliers start: 68 outliers final: 52 residues processed: 243 average time/residue: 0.3364 time to fit residues: 120.7793 Evaluate side-chains 239 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 1.982 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 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 457 ASP 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 54 CYS 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 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 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 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 357 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 79 SER 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 Chi-restraints excluded: chain K residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 134 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN E 137 ASN E 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.174294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119374 restraints weight = 21072.287| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 4.23 r_work: 0.2939 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1997 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= 0.133 Angle : 0.618 14.908 25715 Z= 0.300 Chirality : 0.044 0.309 3109 Planarity : 0.003 0.048 3121 Dihedral : 5.384 51.810 4136 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 3.39 % Allowed : 17.26 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2143 helix: 1.75 (0.29), residues: 402 sheet: 0.31 (0.20), residues: 639 loop : -0.94 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 427 HIS 0.003 0.001 HIS A 216 PHE 0.018 0.001 PHE E 383 TYR 0.011 0.001 TYR G 102 ARG 0.005 0.000 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 45) link_NAG-ASN : angle 2.44835 ( 135) link_BETA1-4 : bond 0.00543 ( 36) link_BETA1-4 : angle 1.20423 ( 108) link_ALPHA1-2 : bond 0.00280 ( 3) link_ALPHA1-2 : angle 1.71756 ( 9) link_ALPHA1-3 : bond 0.01168 ( 3) link_ALPHA1-3 : angle 1.33569 ( 9) hydrogen bonds : bond 0.04325 ( 646) hydrogen bonds : angle 4.29626 ( 1752) SS BOND : bond 0.00664 ( 40) SS BOND : angle 2.37026 ( 80) covalent geometry : bond 0.00327 (18683) covalent geometry : angle 0.57427 (25374) *********************** 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 251 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 186 time to evaluate : 2.128 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8304 (tttp) cc_final: 0.8095 (ttpp) REVERT: B 655 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6658 (ptpt) REVERT: C 69 TRP cc_start: 0.6921 (OUTLIER) cc_final: 0.6201 (m100) REVERT: C 161 MET cc_start: 0.9080 (tpt) cc_final: 0.8796 (mmm) REVERT: E 232 LYS cc_start: 0.8623 (mttp) cc_final: 0.8255 (mmtm) REVERT: G 107 LEU cc_start: 0.5566 (mt) cc_final: 0.5306 (mt) REVERT: H 90 GLN cc_start: 0.6624 (pp30) cc_final: 0.5686 (pp30) REVERT: K 94 THR cc_start: 0.8536 (t) cc_final: 0.8107 (m) outliers start: 65 outliers final: 45 residues processed: 241 average time/residue: 0.3335 time to fit residues: 118.0092 Evaluate side-chains 231 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 1.891 ------------------------------------------------------------------------------- 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 377 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 457 ASP 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 54 CYS 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 613 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 69 TRP 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 413 SER 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 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 Chi-restraints excluded: chain K residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 179 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 151 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3918 r_free = 0.3918 target = 0.171403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.117595 restraints weight = 20939.006| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.74 r_work: 0.2931 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 18810 Z= 0.218 Angle : 0.718 14.417 25715 Z= 0.347 Chirality : 0.047 0.332 3109 Planarity : 0.004 0.053 3121 Dihedral : 5.579 52.001 4136 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.17 % Rotamer: Outliers : 3.39 % Allowed : 17.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2143 helix: 1.58 (0.29), residues: 402 sheet: 0.19 (0.20), residues: 655 loop : -1.06 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.005 0.001 HIS E 85 PHE 0.024 0.002 PHE E 383 TYR 0.014 0.002 TYR A 384 ARG 0.008 0.000 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 45) link_NAG-ASN : angle 2.56035 ( 135) link_BETA1-4 : bond 0.00581 ( 36) link_BETA1-4 : angle 1.30000 ( 108) link_ALPHA1-2 : bond 0.00342 ( 3) link_ALPHA1-2 : angle 1.72896 ( 9) link_ALPHA1-3 : bond 0.01181 ( 3) link_ALPHA1-3 : angle 1.23165 ( 9) hydrogen bonds : bond 0.05495 ( 646) hydrogen bonds : angle 4.46657 ( 1752) SS BOND : bond 0.00616 ( 40) SS BOND : angle 2.75824 ( 80) covalent geometry : bond 0.00558 (18683) covalent geometry : angle 0.67403 (25374) *********************** 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 255 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 2.091 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8509 (tttp) cc_final: 0.8289 (ttpp) REVERT: B 621 GLU cc_start: 0.7729 (mm-30) cc_final: 0.6522 (tm-30) REVERT: B 655 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6791 (ptpt) REVERT: C 69 TRP cc_start: 0.6991 (OUTLIER) cc_final: 0.6560 (m100) REVERT: E 136 ASN cc_start: 0.6663 (m-40) cc_final: 0.5992 (p0) REVERT: E 232 LYS cc_start: 0.8660 (mttp) cc_final: 0.8248 (mmtm) REVERT: G 107 LEU cc_start: 0.5646 (mt) cc_final: 0.5374 (mt) REVERT: H 45 GLN cc_start: 0.6833 (tt0) cc_final: 0.6630 (mt0) REVERT: H 90 GLN cc_start: 0.6987 (pp30) cc_final: 0.6036 (pp30) REVERT: K 76 ASN cc_start: 0.6023 (OUTLIER) cc_final: 0.5630 (m110) REVERT: K 94 THR cc_start: 0.8725 (t) cc_final: 0.8352 (m) REVERT: L 4 MET cc_start: 0.5745 (tpt) cc_final: 0.5460 (tpt) outliers start: 65 outliers final: 56 residues processed: 241 average time/residue: 0.3310 time to fit residues: 119.1671 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 : 2.068 ------------------------------------------------------------------------------- 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 278 THR 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 457 ASP 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 54 CYS 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 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 538 THR 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 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 357 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 605 CYS 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 79 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 94 THR 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 Chi-restraints excluded: chain K residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 124 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 213 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3944 r_free = 0.3944 target = 0.173915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.119176 restraints weight = 21070.671| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.09 r_work: 0.2942 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2170 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= 0.140 Angle : 0.628 14.599 25715 Z= 0.305 Chirality : 0.044 0.315 3109 Planarity : 0.003 0.052 3121 Dihedral : 5.260 52.239 4136 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 3.08 % Allowed : 17.62 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2143 helix: 1.68 (0.29), residues: 402 sheet: 0.29 (0.20), residues: 653 loop : -1.01 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 427 HIS 0.003 0.001 HIS E 85 PHE 0.019 0.001 PHE E 383 TYR 0.012 0.001 TYR G 102 ARG 0.007 0.000 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 45) link_NAG-ASN : angle 2.43909 ( 135) link_BETA1-4 : bond 0.00535 ( 36) link_BETA1-4 : angle 1.18325 ( 108) link_ALPHA1-2 : bond 0.00254 ( 3) link_ALPHA1-2 : angle 1.71897 ( 9) link_ALPHA1-3 : bond 0.01037 ( 3) link_ALPHA1-3 : angle 1.17902 ( 9) hydrogen bonds : bond 0.04400 ( 646) hydrogen bonds : angle 4.29733 ( 1752) SS BOND : bond 0.00586 ( 40) SS BOND : angle 2.48952 ( 80) covalent geometry : bond 0.00349 (18683) covalent geometry : angle 0.58377 (25374) *********************** 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 248 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8701 (mm) REVERT: A 347 LYS cc_start: 0.8441 (tttp) cc_final: 0.8230 (ttpp) REVERT: B 621 GLU cc_start: 0.7695 (mm-30) cc_final: 0.6577 (tm-30) REVERT: B 655 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6764 (ptpt) REVERT: C 69 TRP cc_start: 0.6921 (OUTLIER) cc_final: 0.6308 (m100) REVERT: E 232 LYS cc_start: 0.8630 (mttp) cc_final: 0.8272 (mmtm) REVERT: E 325 ASP cc_start: 0.8347 (t0) cc_final: 0.7977 (t0) REVERT: G 107 LEU cc_start: 0.5630 (mt) cc_final: 0.5357 (mt) REVERT: H 45 GLN cc_start: 0.6822 (tt0) cc_final: 0.6611 (mt0) REVERT: H 90 GLN cc_start: 0.6926 (pp30) cc_final: 0.5998 (pp30) REVERT: K 76 ASN cc_start: 0.5917 (OUTLIER) cc_final: 0.5524 (m110) REVERT: K 94 THR cc_start: 0.8685 (t) cc_final: 0.8312 (m) REVERT: L 4 MET cc_start: 0.5752 (tpt) cc_final: 0.5497 (tpt) outliers start: 59 outliers final: 48 residues processed: 239 average time/residue: 0.3830 time to fit residues: 135.9419 Evaluate side-chains 239 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 2.085 ------------------------------------------------------------------------------- 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 341 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 457 ASP 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 54 CYS 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 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 D residue 639 THR Chi-restraints excluded: chain E residue 69 TRP 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 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 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 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 212 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 161 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 108 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3935 r_free = 0.3935 target = 0.173016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118542 restraints weight = 20933.653| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 4.17 r_work: 0.2945 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18810 Z= 0.163 Angle : 0.662 14.584 25715 Z= 0.321 Chirality : 0.045 0.321 3109 Planarity : 0.004 0.050 3121 Dihedral : 5.252 52.671 4136 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.36 % Rotamer: Outliers : 2.97 % Allowed : 17.94 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2143 helix: 1.67 (0.29), residues: 402 sheet: 0.29 (0.20), residues: 653 loop : -1.03 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 427 HIS 0.004 0.001 HIS E 85 PHE 0.020 0.002 PHE E 383 TYR 0.010 0.001 TYR H 49 ARG 0.007 0.000 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 45) link_NAG-ASN : angle 2.42831 ( 135) link_BETA1-4 : bond 0.00549 ( 36) link_BETA1-4 : angle 1.20018 ( 108) link_ALPHA1-2 : bond 0.00301 ( 3) link_ALPHA1-2 : angle 1.69437 ( 9) link_ALPHA1-3 : bond 0.01057 ( 3) link_ALPHA1-3 : angle 1.13014 ( 9) hydrogen bonds : bond 0.04716 ( 646) hydrogen bonds : angle 4.31774 ( 1752) SS BOND : bond 0.00592 ( 40) SS BOND : angle 2.70300 ( 80) covalent geometry : bond 0.00412 (18683) covalent geometry : angle 0.61863 (25374) ********************** 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 242 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 185 time to evaluate : 1.904 Fit side-chains revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8329 (tttp) cc_final: 0.8116 (ttpp) REVERT: B 621 GLU cc_start: 0.7562 (mm-30) cc_final: 0.6565 (tm-30) REVERT: B 655 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6753 (ptpt) REVERT: C 69 TRP cc_start: 0.6905 (OUTLIER) cc_final: 0.6366 (m100) REVERT: E 136 ASN cc_start: 0.6561 (m-40) cc_final: 0.5890 (p0) REVERT: E 232 LYS cc_start: 0.8616 (mttp) cc_final: 0.8221 (mmtm) REVERT: E 325 ASP cc_start: 0.8235 (t0) cc_final: 0.7905 (t0) REVERT: G 107 LEU cc_start: 0.5640 (mt) cc_final: 0.5376 (mt) REVERT: H 90 GLN cc_start: 0.6719 (pp30) cc_final: 0.5806 (pp30) REVERT: K 76 ASN cc_start: 0.5884 (OUTLIER) cc_final: 0.5509 (m110) REVERT: K 94 THR cc_start: 0.8569 (t) cc_final: 0.8183 (m) outliers start: 57 outliers final: 52 residues processed: 233 average time/residue: 0.3212 time to fit residues: 110.9896 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 : 2.117 ------------------------------------------------------------------------------- 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 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 457 ASP 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 54 CYS 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 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 D residue 639 THR Chi-restraints excluded: chain E residue 69 TRP 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 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 639 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 79 SER 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 76 ASN Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 52 optimal weight: 0.5980 chunk 210 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 175 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3938 r_free = 0.3938 target = 0.173342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118719 restraints weight = 20899.530| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 4.11 r_work: 0.2994 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2300 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= 0.158 Angle : 0.657 14.532 25715 Z= 0.318 Chirality : 0.044 0.319 3109 Planarity : 0.004 0.058 3121 Dihedral : 5.177 52.768 4136 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 3.23 % Allowed : 17.67 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2143 helix: 1.67 (0.29), residues: 402 sheet: 0.29 (0.20), residues: 653 loop : -1.03 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 427 HIS 0.004 0.001 HIS E 85 PHE 0.019 0.002 PHE E 383 TYR 0.011 0.001 TYR G 102 ARG 0.007 0.000 ARG D 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 45) link_NAG-ASN : angle 2.42854 ( 135) link_BETA1-4 : bond 0.00546 ( 36) link_BETA1-4 : angle 1.18305 ( 108) link_ALPHA1-2 : bond 0.00293 ( 3) link_ALPHA1-2 : angle 1.68586 ( 9) link_ALPHA1-3 : bond 0.01006 ( 3) link_ALPHA1-3 : angle 1.09429 ( 9) hydrogen bonds : bond 0.04621 ( 646) hydrogen bonds : angle 4.31076 ( 1752) SS BOND : bond 0.00582 ( 40) SS BOND : angle 2.63849 ( 80) covalent geometry : bond 0.00397 (18683) covalent geometry : angle 0.61344 (25374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9978.25 seconds wall clock time: 173 minutes 13.84 seconds (10393.84 seconds total)