Starting phenix.real_space_refine on Tue Nov 19 03:24:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl2_41359/11_2024/8tl2_41359.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl2_41359/11_2024/8tl2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl2_41359/11_2024/8tl2_41359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl2_41359/11_2024/8tl2_41359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl2_41359/11_2024/8tl2_41359.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl2_41359/11_2024/8tl2_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-5513/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: 12.08, per 1000 atoms: 0.66 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: 5.61 Conformation dependent library (CDL) restraints added in 2.3 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: 2.73 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: 7.02 Time building geometry restraints manager: 6.40 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: 0.010 Normalize map: mean=0, sd=1: 6.050 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: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 45.990 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.150 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.100 ------------------------------------------------------------------------------- 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 18683 Z= 0.299 Angle : 0.728 17.831 25374 Z= 0.345 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 *********************** 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 : 1.950 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: 0.3784 time to fit residues: 102.7986 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 : 2.054 ------------------------------------------------------------------------------- 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: 0.3980 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: 1.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 18683 Z= 0.371 Angle : 0.711 15.945 25374 Z= 0.351 Chirality : 0.048 0.318 3109 Planarity : 0.004 0.049 3121 Dihedral : 9.785 73.351 4136 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 2.29 % Allowed : 14.65 % Favored : 83.06 % 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: -0.07 (0.18), residues: 2143 helix: 1.71 (0.29), residues: 414 sheet: 0.17 (0.20), residues: 649 loop : -0.87 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 0.006 0.001 ARG D 542 *********************** 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 235 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 1.820 Fit side-chains revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8249 (mpt-90) REVERT: B 655 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6820 (ptpt) REVERT: C 117 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7947 (mmtm) REVERT: E 54 CYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6615 (t) REVERT: E 271 MET cc_start: 0.9071 (mmm) cc_final: 0.8635 (mmt) REVERT: G 107 LEU cc_start: 0.5835 (mt) cc_final: 0.5548 (mt) outliers start: 44 outliers final: 21 residues processed: 225 average time/residue: 0.3504 time to fit residues: 116.5500 Evaluate side-chains 208 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 308 ARG 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 109 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 164 optimal weight: 0.0670 chunk 134 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 175 optimal weight: 0.0970 chunk 195 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- 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 C 67 ASN E 137 ASN G 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18683 Z= 0.173 Angle : 0.556 14.819 25374 Z= 0.280 Chirality : 0.043 0.285 3109 Planarity : 0.003 0.052 3121 Dihedral : 7.858 59.875 4136 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.24 % Favored : 97.71 % Rotamer: Outliers : 2.29 % Allowed : 15.90 % Favored : 81.80 % 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: 0.05 (0.18), residues: 2143 helix: 1.98 (0.29), residues: 402 sheet: 0.28 (0.20), residues: 634 loop : -0.84 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.004 0.000 ARG D 542 *********************** 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 234 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 2.001 Fit side-chains REVERT: B 655 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.6903 (ptpt) REVERT: C 117 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7843 (mmtm) REVERT: G 107 LEU cc_start: 0.5838 (mt) cc_final: 0.5573 (mt) outliers start: 44 outliers final: 28 residues processed: 222 average time/residue: 0.3493 time to fit residues: 114.0507 Evaluate side-chains 213 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 2.074 ------------------------------------------------------------------------------- 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 396 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 445 CYS 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 357 THR 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 54 CYS Chi-restraints excluded: chain E residue 184 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 0.0470 chunk 132 optimal weight: 2.9990 chunk 198 optimal weight: 0.0020 chunk 209 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 187 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 overall best weight: 1.1090 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18683 Z= 0.267 Angle : 0.598 12.466 25374 Z= 0.300 Chirality : 0.045 0.301 3109 Planarity : 0.004 0.045 3121 Dihedral : 6.811 56.602 4136 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 3.02 % Allowed : 15.54 % Favored : 81.44 % 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: 1.84 (0.29), residues: 402 sheet: 0.32 (0.20), residues: 630 loop : -0.90 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 427 HIS 0.004 0.001 HIS E 85 PHE 0.019 0.002 PHE E 383 TYR 0.011 0.001 TYR H 49 ARG 0.007 0.000 ARG D 542 *********************** 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 247 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 2.040 Fit side-chains revert: symmetry clash REVERT: B 655 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6929 (ptpt) REVERT: C 117 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7869 (mmtm) REVERT: C 455 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8725 (p) REVERT: E 54 CYS cc_start: 0.6713 (OUTLIER) cc_final: 0.6152 (t) REVERT: G 107 LEU cc_start: 0.5870 (mt) cc_final: 0.5589 (mt) REVERT: H 45 GLN cc_start: 0.6983 (tt0) cc_final: 0.6601 (mt0) REVERT: H 90 GLN cc_start: 0.7441 (pp30) cc_final: 0.6618 (pp30) REVERT: H 92 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7876 (tm-30) REVERT: K 94 THR cc_start: 0.8723 (t) cc_final: 0.8355 (m) outliers start: 58 outliers final: 39 residues processed: 235 average time/residue: 0.3498 time to fit residues: 121.1062 Evaluate side-chains 228 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 377 ASN Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 117 LYS 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 455 THR 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 54 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 413 SER Chi-restraints excluded: chain F residue 612 SER 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 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 174 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 178 optimal weight: 0.0970 chunk 144 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 188 optimal weight: 0.0470 chunk 52 optimal weight: 4.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 18683 Z= 0.172 Angle : 0.533 14.478 25374 Z= 0.270 Chirality : 0.043 0.292 3109 Planarity : 0.003 0.047 3121 Dihedral : 5.773 50.681 4136 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Rotamer: Outliers : 2.87 % Allowed : 16.58 % Favored : 80.55 % 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: 1.93 (0.29), residues: 402 sheet: 0.45 (0.20), residues: 630 loop : -0.87 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 427 HIS 0.004 0.001 HIS A 216 PHE 0.016 0.001 PHE E 383 TYR 0.011 0.001 TYR H 49 ARG 0.006 0.000 ARG E 500 *********************** 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 249 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 194 time to evaluate : 2.021 Fit side-chains revert: symmetry clash REVERT: B 544 LEU cc_start: 0.9201 (mm) cc_final: 0.8965 (mt) REVERT: B 655 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.6940 (ptpt) REVERT: C 117 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7779 (mmtm) REVERT: E 232 LYS cc_start: 0.8601 (mttp) cc_final: 0.8316 (mmtm) REVERT: G 107 LEU cc_start: 0.5843 (mt) cc_final: 0.5569 (mt) REVERT: H 90 GLN cc_start: 0.7358 (pp30) cc_final: 0.6547 (pp30) REVERT: H 92 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7893 (tm-30) REVERT: K 94 THR cc_start: 0.8739 (t) cc_final: 0.8382 (m) outliers start: 55 outliers final: 40 residues processed: 235 average time/residue: 0.3506 time to fit residues: 121.5665 Evaluate side-chains 231 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 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 655 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 433 CYS 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 172 VAL Chi-restraints excluded: chain E residue 184 ILE 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 518 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 80 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 209 optimal weight: 9.9990 chunk 174 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 18683 Z= 0.196 Angle : 0.547 13.165 25374 Z= 0.276 Chirality : 0.043 0.294 3109 Planarity : 0.003 0.043 3121 Dihedral : 5.321 51.215 4136 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Rotamer: Outliers : 2.97 % Allowed : 16.58 % Favored : 80.45 % 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: 1.87 (0.29), residues: 405 sheet: 0.49 (0.20), residues: 630 loop : -0.89 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 427 HIS 0.003 0.001 HIS A 216 PHE 0.017 0.001 PHE E 383 TYR 0.010 0.001 TYR H 49 ARG 0.007 0.000 ARG E 500 *********************** 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 242 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 185 time to evaluate : 1.805 Fit side-chains revert: symmetry clash REVERT: B 544 LEU cc_start: 0.9207 (mm) cc_final: 0.8968 (mt) REVERT: B 655 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6858 (ptpt) REVERT: C 69 TRP cc_start: 0.7109 (OUTLIER) cc_final: 0.6533 (m100) REVERT: C 117 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7839 (mmtm) REVERT: C 455 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8721 (p) REVERT: E 232 LYS cc_start: 0.8599 (mttp) cc_final: 0.8274 (mmtm) REVERT: G 107 LEU cc_start: 0.5830 (mt) cc_final: 0.5564 (mt) REVERT: H 90 GLN cc_start: 0.7353 (pp30) cc_final: 0.6597 (pp30) REVERT: H 92 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7924 (tm-30) REVERT: K 94 THR cc_start: 0.8731 (t) cc_final: 0.8392 (m) outliers start: 57 outliers final: 44 residues processed: 229 average time/residue: 0.3494 time to fit residues: 118.3487 Evaluate side-chains 230 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain C residue 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 117 LYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 455 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 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 518 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 4 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 209 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 18683 Z= 0.353 Angle : 0.663 12.627 25374 Z= 0.331 Chirality : 0.047 0.321 3109 Planarity : 0.004 0.047 3121 Dihedral : 5.491 51.446 4135 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.64 % Favored : 96.27 % Rotamer: Outliers : 3.60 % Allowed : 16.68 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.69 (0.29), residues: 402 sheet: 0.34 (0.20), residues: 633 loop : -1.02 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 427 HIS 0.005 0.001 HIS E 85 PHE 0.023 0.002 PHE E 383 TYR 0.015 0.002 TYR A 384 ARG 0.004 0.000 ARG E 151 *********************** 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 265 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 196 time to evaluate : 1.916 Fit side-chains revert: symmetry clash REVERT: B 544 LEU cc_start: 0.9279 (mm) cc_final: 0.9035 (mt) REVERT: B 655 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.6761 (ptpt) REVERT: C 69 TRP cc_start: 0.7069 (OUTLIER) cc_final: 0.6746 (m100) REVERT: C 117 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8068 (mmtm) REVERT: C 455 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8744 (p) REVERT: E 136 ASN cc_start: 0.6622 (m-40) cc_final: 0.6119 (p0) REVERT: E 232 LYS cc_start: 0.8635 (mttp) cc_final: 0.8241 (mmtm) REVERT: G 107 LEU cc_start: 0.5894 (mt) cc_final: 0.5642 (mt) REVERT: H 45 GLN cc_start: 0.7054 (tt0) cc_final: 0.6760 (mt0) REVERT: H 90 GLN cc_start: 0.7364 (pp30) cc_final: 0.6542 (pp30) REVERT: H 92 GLN cc_start: 0.8224 (tm-30) cc_final: 0.8021 (tm-30) REVERT: K 94 THR cc_start: 0.8769 (t) cc_final: 0.8426 (m) outliers start: 69 outliers final: 49 residues processed: 250 average time/residue: 0.3365 time to fit residues: 124.8519 Evaluate side-chains 246 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 1.949 ------------------------------------------------------------------------------- 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 340 GLU 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 68 VAL Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 117 LYS 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 455 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 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 501 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 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 129 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 164 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 H 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 18683 Z= 0.191 Angle : 0.563 14.741 25374 Z= 0.283 Chirality : 0.043 0.299 3109 Planarity : 0.003 0.045 3121 Dihedral : 5.114 52.016 4135 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.25 % Rotamer: Outliers : 2.87 % Allowed : 17.62 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.84 (0.29), residues: 402 sheet: 0.37 (0.20), residues: 650 loop : -0.92 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 427 HIS 0.004 0.001 HIS A 216 PHE 0.017 0.001 PHE E 383 TYR 0.012 0.001 TYR G 102 ARG 0.009 0.000 ARG D 542 *********************** 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 240 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 2.251 Fit side-chains revert: symmetry clash REVERT: B 544 LEU cc_start: 0.9256 (mm) cc_final: 0.9024 (mt) REVERT: B 655 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6819 (ptpt) REVERT: C 69 TRP cc_start: 0.7109 (OUTLIER) cc_final: 0.6416 (m100) REVERT: C 117 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7986 (mmtm) REVERT: C 455 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8723 (p) REVERT: E 232 LYS cc_start: 0.8599 (mttp) cc_final: 0.8296 (mmtm) REVERT: E 325 ASP cc_start: 0.8050 (t0) cc_final: 0.7746 (t0) REVERT: F 544 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8935 (mt) REVERT: G 107 LEU cc_start: 0.5850 (mt) cc_final: 0.5601 (mt) REVERT: H 45 GLN cc_start: 0.7033 (tt0) cc_final: 0.6751 (mt0) REVERT: H 90 GLN cc_start: 0.7327 (pp30) cc_final: 0.6596 (pp30) REVERT: H 92 GLN cc_start: 0.8218 (tm-30) cc_final: 0.8012 (tm-30) REVERT: K 94 THR cc_start: 0.8765 (t) cc_final: 0.8439 (m) outliers start: 55 outliers final: 43 residues processed: 230 average time/residue: 0.3485 time to fit residues: 118.8937 Evaluate side-chains 235 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 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 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 117 LYS 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 207 LYS Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 455 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 172 VAL 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 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 501 CYS Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 544 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 H residue 46 LEU Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 80 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 127 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 18683 Z= 0.507 Angle : 0.754 15.429 25374 Z= 0.373 Chirality : 0.050 0.344 3109 Planarity : 0.005 0.049 3121 Dihedral : 5.671 51.907 4135 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.89 % Rotamer: Outliers : 3.34 % Allowed : 17.47 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.18), residues: 2143 helix: 1.48 (0.29), residues: 402 sheet: 0.15 (0.20), residues: 655 loop : -1.10 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 427 HIS 0.007 0.002 HIS E 85 PHE 0.029 0.002 PHE C 383 TYR 0.019 0.002 TYR A 384 ARG 0.008 0.001 ARG D 542 *********************** 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 249 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 2.162 Fit side-chains revert: symmetry clash REVERT: B 544 LEU cc_start: 0.9266 (mm) cc_final: 0.9042 (mt) REVERT: B 621 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6649 (tm-30) REVERT: B 655 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6673 (ptpt) REVERT: C 69 TRP cc_start: 0.7086 (OUTLIER) cc_final: 0.6828 (m100) REVERT: C 455 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8747 (p) REVERT: E 136 ASN cc_start: 0.6805 (m-40) cc_final: 0.6343 (p0) REVERT: E 232 LYS cc_start: 0.8679 (mttp) cc_final: 0.8289 (mmtm) REVERT: G 107 LEU cc_start: 0.5997 (mt) cc_final: 0.5738 (mt) REVERT: H 45 GLN cc_start: 0.7130 (tt0) cc_final: 0.6785 (mt0) REVERT: H 90 GLN cc_start: 0.7415 (pp30) cc_final: 0.6591 (pp30) REVERT: H 92 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7982 (tm-30) REVERT: K 94 THR cc_start: 0.8764 (t) cc_final: 0.8452 (m) outliers start: 64 outliers final: 50 residues processed: 238 average time/residue: 0.3167 time to fit residues: 112.2123 Evaluate side-chains 239 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 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 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 C residue 455 THR 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 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 501 CYS Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain G residue 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 198 optimal weight: 0.0370 chunk 172 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 18683 Z= 0.210 Angle : 0.590 15.102 25374 Z= 0.295 Chirality : 0.044 0.309 3109 Planarity : 0.003 0.046 3121 Dihedral : 5.240 52.178 4135 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.97 % Rotamer: Outliers : 2.50 % Allowed : 18.14 % 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: -0.13 (0.18), residues: 2143 helix: 1.69 (0.29), residues: 402 sheet: 0.27 (0.20), residues: 653 loop : -1.00 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 427 HIS 0.004 0.001 HIS A 216 PHE 0.017 0.001 PHE E 383 TYR 0.013 0.001 TYR C 173 ARG 0.007 0.000 ARG D 542 ********************** 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 240 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 2.422 Fit side-chains revert: symmetry clash REVERT: B 544 LEU cc_start: 0.9250 (mm) cc_final: 0.9039 (mt) REVERT: B 621 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6770 (tm-30) REVERT: B 655 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6844 (ptpt) REVERT: C 69 TRP cc_start: 0.7098 (OUTLIER) cc_final: 0.6485 (m100) REVERT: C 161 MET cc_start: 0.9114 (tpt) cc_final: 0.8893 (mmm) REVERT: C 455 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8732 (p) REVERT: E 117 LYS cc_start: 0.8434 (ttmm) cc_final: 0.7940 (mmtt) REVERT: E 232 LYS cc_start: 0.8614 (mttp) cc_final: 0.8300 (mmtm) REVERT: G 107 LEU cc_start: 0.5901 (mt) cc_final: 0.5651 (mt) REVERT: H 45 GLN cc_start: 0.7072 (tt0) cc_final: 0.6760 (mt0) REVERT: H 90 GLN cc_start: 0.7368 (pp30) cc_final: 0.6563 (pp30) REVERT: H 92 GLN cc_start: 0.8212 (tm-30) cc_final: 0.8005 (tm-30) REVERT: K 94 THR cc_start: 0.8755 (t) cc_final: 0.8449 (m) outliers start: 48 outliers final: 42 residues processed: 233 average time/residue: 0.3565 time to fit residues: 122.8540 Evaluate side-chains 233 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.791 ------------------------------------------------------------------------------- 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 308 ARG Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 377 ASN 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 433 CYS Chi-restraints excluded: chain C residue 455 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 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 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 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 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 5.9990 chunk 52 optimal weight: 0.0470 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 172 optimal weight: 9.9990 chunk 72 optimal weight: 0.5980 chunk 177 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.4680 ------------------------------------------------------------------------------- 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 E 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.176708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.122018 restraints weight = 20731.578| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 4.38 r_work: 0.2975 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18683 Z= 0.167 Angle : 0.549 15.017 25374 Z= 0.275 Chirality : 0.042 0.301 3109 Planarity : 0.003 0.044 3121 Dihedral : 4.824 53.318 4135 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 2.35 % Allowed : 18.56 % 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: 0.06 (0.18), residues: 2143 helix: 1.88 (0.29), residues: 402 sheet: 0.41 (0.20), residues: 650 loop : -0.91 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 427 HIS 0.004 0.001 HIS A 216 PHE 0.016 0.001 PHE E 383 TYR 0.011 0.001 TYR H 49 ARG 0.007 0.000 ARG D 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3900.58 seconds wall clock time: 96 minutes 51.35 seconds (5811.35 seconds total)