Starting phenix.real_space_refine on Sat Sep 28 18:34:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkc_41346/09_2024/8tkc_41346.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkc_41346/09_2024/8tkc_41346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkc_41346/09_2024/8tkc_41346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkc_41346/09_2024/8tkc_41346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkc_41346/09_2024/8tkc_41346.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkc_41346/09_2024/8tkc_41346.cif" } resolution = 3.1 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= 0.041 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 123 5.16 5 C 12549 2.51 5 N 3336 2.21 5 O 4056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20064 Number of models: 1 Model: "" Number of chains: 45 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: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 980 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "H" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 99} Chain: "I" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 980 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "J" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 99} Chain: "K" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 980 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 99} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" 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: "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: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 14.26, per 1000 atoms: 0.71 Number of scatterers: 20064 At special positions: 0 Unit cell: (150.284, 142.51, 124.373, 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 123 16.00 O 4056 8.00 N 3336 7.00 C 12549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 R 4 " - " MAN R 5 " " MAN b 4 " - " MAN b 5 " " MAN m 4 " - " MAN m 5 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA m 3 " - " MAN m 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 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 M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 276 " " NAG Z 1 " - " ASN C 386 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 295 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 332 " " NAG f 1 " - " ASN C 363 " " NAG g 1 " - " ASN E 295 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 386 " " NAG m 1 " - " ASN E 262 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 332 " " NAG p 1 " - " ASN E 363 " Time building additional restraints: 6.02 Conformation dependent library (CDL) restraints added in 2.4 seconds 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 41 sheets defined 19.0% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.122A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.597A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.253A 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 543 removed outlier: 3.882A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.595A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.887A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 663 removed outlier: 3.724A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.162A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.551A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.920A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'D' and resid 521 through 527 removed outlier: 4.595A pdb=" N ALA D 525 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 4.323A 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: 3.985A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 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 663 removed outlier: 3.729A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.178A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.547A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 195 through 198 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: 3.505A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 527 removed outlier: 4.549A pdb=" N ALA F 525 " --> pdb=" O PHE F 522 " (cutoff:3.500A) removed outlier: 4.182A 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: 4.088A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.552A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.903A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 639 through 663 removed outlier: 3.750A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.869A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.863A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.860A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.314A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.482A 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: 4.039A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.567A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.398A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.144A 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: 7.051A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.600A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.571A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'B' and resid 516 through 519 removed outlier: 6.186A pdb=" N GLY B 516 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TYR G 99 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 518 " --> pdb=" O TYR G 99 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN G 95 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TYR G 34 " --> pdb=" O GLN G 95 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.596A pdb=" N VAL G 12 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.311A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.831A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.407A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.032A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.401A 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: 10.616A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.581A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 517 through 519 removed outlier: 6.646A pdb=" N VAL D 518 " --> pdb=" O TYR I 99 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN I 95 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR I 34 " --> pdb=" O GLN I 95 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP I 35 " --> pdb=" O ASN I 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.600A pdb=" N VAL I 12 " --> pdb=" O SER I 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.293A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.065A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.418A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.030A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.506A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.590A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD4, first strand: chain 'F' and resid 517 through 519 removed outlier: 6.737A pdb=" N VAL F 518 " --> pdb=" O TYR K 99 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN K 95 " --> pdb=" O TYR K 34 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR K 34 " --> pdb=" O GLN K 95 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP K 35 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN K 50 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.605A pdb=" N VAL K 12 " --> pdb=" O SER K 112 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.536A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.538A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.539A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 1974 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: 7.53 Time building geometry restraints manager: 6.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.26: 3199 1.26 - 1.61: 17107 1.61 - 1.97: 162 1.97 - 2.32: 0 2.32 - 2.67: 1 Bond restraints: 20469 Sorted by residual: bond pdb=" CB PRO A 498 " pdb=" CG PRO A 498 " ideal model delta sigma weight residual 1.492 2.675 -1.183 5.00e-02 4.00e+02 5.60e+02 bond pdb=" CG PRO A 498 " pdb=" CD PRO A 498 " ideal model delta sigma weight residual 1.503 0.908 0.595 3.40e-02 8.65e+02 3.06e+02 bond pdb=" C ALA A 497 " pdb=" N PRO A 498 " ideal model delta sigma weight residual 1.329 1.420 -0.090 1.25e-02 6.40e+03 5.22e+01 bond pdb=" CA PRO A 498 " pdb=" CB PRO A 498 " ideal model delta sigma weight residual 1.534 1.454 0.080 1.23e-02 6.61e+03 4.22e+01 bond pdb=" N PRO A 498 " pdb=" CD PRO A 498 " ideal model delta sigma weight residual 1.473 1.563 -0.090 1.40e-02 5.10e+03 4.17e+01 ... (remaining 20464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.92: 27806 19.92 - 39.84: 0 39.84 - 59.76: 0 59.76 - 79.68: 0 79.68 - 99.60: 1 Bond angle restraints: 27807 Sorted by residual: angle pdb=" CB PRO A 498 " pdb=" CG PRO A 498 " pdb=" CD PRO A 498 " ideal model delta sigma weight residual 106.10 6.50 99.60 3.20e+00 9.77e-02 9.69e+02 angle pdb=" N PRO A 498 " pdb=" CA PRO A 498 " pdb=" CB PRO A 498 " ideal model delta sigma weight residual 103.15 92.10 11.05 9.70e-01 1.06e+00 1.30e+02 angle pdb=" CA PRO A 498 " pdb=" CB PRO A 498 " pdb=" CG PRO A 498 " ideal model delta sigma weight residual 104.50 87.00 17.50 1.90e+00 2.77e-01 8.48e+01 angle pdb=" CA PRO A 498 " pdb=" N PRO A 498 " pdb=" CD PRO A 498 " ideal model delta sigma weight residual 112.00 100.68 11.32 1.40e+00 5.10e-01 6.54e+01 angle pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 114.40 132.09 -17.69 2.30e+00 1.89e-01 5.92e+01 ... (remaining 27802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.42: 12513 27.42 - 54.84: 686 54.84 - 82.26: 114 82.26 - 109.68: 42 109.68 - 137.10: 1 Dihedral angle restraints: 13356 sinusoidal: 6408 harmonic: 6948 Sorted by residual: 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 5.18 87.82 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual 93.00 26.04 66.96 1 1.00e+01 1.00e-02 5.84e+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 -86.00 -21.97 -64.03 1 1.00e+01 1.00e-02 5.40e+01 ... (remaining 13353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2891 0.062 - 0.124: 403 0.124 - 0.187: 70 0.187 - 0.249: 2 0.249 - 0.311: 12 Chirality restraints: 3378 Sorted by residual: chirality pdb=" CA CYS E 296 " pdb=" N CYS E 296 " pdb=" C CYS E 296 " pdb=" CB CYS E 296 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+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 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 3375 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 239 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO C 240 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 240 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 240 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER I 100F" -0.038 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO I 100G" 0.101 5.00e-02 4.00e+02 pdb=" CA PRO I 100G" -0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 100G" -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 100F" -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO G 100G" 0.100 5.00e-02 4.00e+02 pdb=" CA PRO G 100G" -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 100G" -0.031 5.00e-02 4.00e+02 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 396 2.69 - 3.24: 17654 3.24 - 3.79: 28755 3.79 - 4.35: 39112 4.35 - 4.90: 67608 Nonbonded interactions: 153525 Sorted by model distance: nonbonded pdb=" OG1 THR A 139 " pdb=" OD1 ASP A 141 " model vdw 2.134 3.040 nonbonded pdb=" O PHE D 522 " pdb=" NE2 GLN D 540 " model vdw 2.188 3.120 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.194 3.040 nonbonded pdb=" O ASP H 82 " pdb=" OH TYR H 86 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR C 139 " pdb=" OD1 ASP C 141 " model vdw 2.223 3.040 ... (remaining 153520 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 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'j' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 50.350 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.011 1.183 20469 Z= 0.646 Angle : 0.954 99.605 27807 Z= 0.410 Chirality : 0.049 0.311 3378 Planarity : 0.004 0.060 3429 Dihedral : 16.986 137.102 8754 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.61 % Favored : 97.26 % Rotamer: Outliers : 0.33 % Allowed : 13.44 % Favored : 86.23 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.00 (0.17), residues: 2373 helix: 2.24 (0.29), residues: 396 sheet: 0.15 (0.18), residues: 777 loop : -0.87 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.004 0.001 HIS A 216 PHE 0.010 0.001 PHE A 53 TYR 0.036 0.001 TYR I 34 ARG 0.007 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 GLU cc_start: 0.7881 (tp30) cc_final: 0.7666 (tp30) REVERT: C 268 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6719 (pm20) REVERT: E 268 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6627 (pm20) REVERT: E 475 MET cc_start: 0.8836 (mmp) cc_final: 0.8611 (tpp) REVERT: F 655 LYS cc_start: 0.6394 (ttpt) cc_final: 0.5967 (ttpt) outliers start: 7 outliers final: 5 residues processed: 182 average time/residue: 0.4286 time to fit residues: 110.1303 Evaluate side-chains 175 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain I residue 100 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 8.9990 chunk 179 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 185 optimal weight: 30.0000 chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 653 GLN E 137 ASN E 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.014 20469 Z= 0.710 Angle : 0.992 106.100 27807 Z= 0.435 Chirality : 0.050 0.256 3378 Planarity : 0.005 0.072 3429 Dihedral : 11.824 92.449 4377 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.16 % Favored : 96.71 % Rotamer: Outliers : 1.98 % Allowed : 13.15 % Favored : 84.87 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.17), residues: 2373 helix: 1.75 (0.28), residues: 399 sheet: 0.16 (0.18), residues: 801 loop : -0.97 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 427 HIS 0.004 0.001 HIS C 374 PHE 0.022 0.002 PHE A 383 TYR 0.013 0.002 TYR L 49 ARG 0.007 0.001 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 174 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8070 (tt0) cc_final: 0.7717 (tt0) REVERT: E 268 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6809 (pm20) REVERT: E 426 MET cc_start: 0.7377 (tpp) cc_final: 0.7131 (tpt) REVERT: F 655 LYS cc_start: 0.6680 (ttpt) cc_final: 0.6227 (ttpt) REVERT: H 4 MET cc_start: 0.4633 (mmm) cc_final: 0.3885 (ttt) REVERT: L 33 LEU cc_start: 0.5285 (OUTLIER) cc_final: 0.4931 (tp) REVERT: L 85 THR cc_start: 0.4112 (OUTLIER) cc_final: 0.3772 (m) outliers start: 42 outliers final: 22 residues processed: 207 average time/residue: 0.4078 time to fit residues: 122.4577 Evaluate side-chains 194 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 179 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 213 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 172 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 C 355 ASN D 653 GLN E 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.039 20469 Z= 0.582 Angle : 0.937 106.100 27807 Z= 0.407 Chirality : 0.045 0.380 3378 Planarity : 0.005 0.076 3429 Dihedral : 11.670 92.411 4370 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 1.74 % Allowed : 14.24 % Favored : 84.02 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2373 helix: 1.86 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 801 loop : -1.00 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.003 0.001 HIS C 374 PHE 0.044 0.002 PHE G 100H TYR 0.013 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 170 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8022 (tt0) cc_final: 0.7675 (tt0) REVERT: C 268 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6637 (pm20) REVERT: E 268 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6760 (pm20) REVERT: E 426 MET cc_start: 0.7368 (tpp) cc_final: 0.7129 (tpt) REVERT: H 4 MET cc_start: 0.4605 (mmm) cc_final: 0.3839 (ttt) REVERT: L 33 LEU cc_start: 0.5278 (OUTLIER) cc_final: 0.4911 (tp) outliers start: 37 outliers final: 27 residues processed: 196 average time/residue: 0.4069 time to fit residues: 113.9495 Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 216 optimal weight: 30.0000 chunk 229 optimal weight: 20.0000 chunk 113 optimal weight: 0.7980 chunk 205 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.039 20469 Z= 0.582 Angle : 0.937 106.100 27807 Z= 0.407 Chirality : 0.045 0.380 3378 Planarity : 0.005 0.076 3429 Dihedral : 11.670 92.411 4370 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 1.32 % Allowed : 14.52 % Favored : 84.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2373 helix: 1.86 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 801 loop : -1.00 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.003 0.001 HIS C 374 PHE 0.044 0.002 PHE G 100H TYR 0.013 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8023 (tt0) cc_final: 0.7675 (tt0) REVERT: C 268 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6637 (pm20) REVERT: E 268 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6760 (pm20) REVERT: E 426 MET cc_start: 0.7368 (tpp) cc_final: 0.7129 (tpt) REVERT: H 4 MET cc_start: 0.4604 (mmm) cc_final: 0.3839 (ttt) REVERT: L 33 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.4911 (tp) outliers start: 28 outliers final: 27 residues processed: 185 average time/residue: 0.4562 time to fit residues: 121.4400 Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 0.1980 chunk 130 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 94 optimal weight: 0.0030 chunk 195 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.039 20469 Z= 0.582 Angle : 0.937 106.100 27807 Z= 0.407 Chirality : 0.045 0.380 3378 Planarity : 0.005 0.076 3429 Dihedral : 11.670 92.411 4370 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 1.32 % Allowed : 14.52 % Favored : 84.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2373 helix: 1.86 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 801 loop : -1.00 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.003 0.001 HIS C 374 PHE 0.044 0.002 PHE G 100H TYR 0.013 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8023 (tt0) cc_final: 0.7675 (tt0) REVERT: C 268 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6637 (pm20) REVERT: E 268 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6760 (pm20) REVERT: E 426 MET cc_start: 0.7368 (tpp) cc_final: 0.7129 (tpt) REVERT: H 4 MET cc_start: 0.4604 (mmm) cc_final: 0.3839 (ttt) REVERT: L 33 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.4911 (tp) outliers start: 28 outliers final: 27 residues processed: 185 average time/residue: 0.4323 time to fit residues: 114.8489 Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 134 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.039 20469 Z= 0.582 Angle : 0.937 106.100 27807 Z= 0.407 Chirality : 0.045 0.380 3378 Planarity : 0.005 0.076 3429 Dihedral : 11.670 92.411 4370 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 1.32 % Allowed : 14.52 % Favored : 84.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2373 helix: 1.86 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 801 loop : -1.00 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.003 0.001 HIS C 374 PHE 0.044 0.002 PHE G 100H TYR 0.013 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8023 (tt0) cc_final: 0.7675 (tt0) REVERT: C 268 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6637 (pm20) REVERT: E 268 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6760 (pm20) REVERT: E 426 MET cc_start: 0.7368 (tpp) cc_final: 0.7129 (tpt) REVERT: H 4 MET cc_start: 0.4604 (mmm) cc_final: 0.3839 (ttt) REVERT: L 33 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.4911 (tp) outliers start: 28 outliers final: 27 residues processed: 185 average time/residue: 0.4321 time to fit residues: 114.0707 Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 129 optimal weight: 0.3980 chunk 193 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 228 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.039 20469 Z= 0.582 Angle : 0.937 106.100 27807 Z= 0.407 Chirality : 0.045 0.380 3378 Planarity : 0.005 0.076 3429 Dihedral : 11.670 92.411 4370 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 1.32 % Allowed : 14.52 % Favored : 84.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2373 helix: 1.86 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 801 loop : -1.00 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.003 0.001 HIS C 374 PHE 0.044 0.002 PHE G 100H TYR 0.013 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8023 (tt0) cc_final: 0.7675 (tt0) REVERT: C 268 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6637 (pm20) REVERT: E 268 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6760 (pm20) REVERT: E 426 MET cc_start: 0.7368 (tpp) cc_final: 0.7129 (tpt) REVERT: H 4 MET cc_start: 0.4604 (mmm) cc_final: 0.3839 (ttt) REVERT: L 33 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.4911 (tp) outliers start: 28 outliers final: 27 residues processed: 185 average time/residue: 0.4244 time to fit residues: 111.6469 Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.039 20469 Z= 0.582 Angle : 0.937 106.100 27807 Z= 0.407 Chirality : 0.045 0.380 3378 Planarity : 0.005 0.076 3429 Dihedral : 11.670 92.411 4370 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 1.32 % Allowed : 14.52 % Favored : 84.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2373 helix: 1.86 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 801 loop : -1.00 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.003 0.001 HIS C 374 PHE 0.044 0.002 PHE G 100H TYR 0.013 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8023 (tt0) cc_final: 0.7675 (tt0) REVERT: C 268 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6637 (pm20) REVERT: E 268 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6760 (pm20) REVERT: E 426 MET cc_start: 0.7368 (tpp) cc_final: 0.7129 (tpt) REVERT: H 4 MET cc_start: 0.4604 (mmm) cc_final: 0.3839 (ttt) REVERT: L 33 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.4911 (tp) outliers start: 28 outliers final: 27 residues processed: 185 average time/residue: 0.4122 time to fit residues: 108.5044 Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 212 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 167 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 192 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.039 20469 Z= 0.582 Angle : 0.937 106.100 27807 Z= 0.407 Chirality : 0.045 0.380 3378 Planarity : 0.005 0.076 3429 Dihedral : 11.670 92.411 4370 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 1.32 % Allowed : 14.52 % Favored : 84.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2373 helix: 1.86 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 801 loop : -1.00 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.003 0.001 HIS C 374 PHE 0.044 0.002 PHE G 100H TYR 0.013 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8023 (tt0) cc_final: 0.7675 (tt0) REVERT: C 268 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6637 (pm20) REVERT: E 268 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6760 (pm20) REVERT: E 426 MET cc_start: 0.7368 (tpp) cc_final: 0.7129 (tpt) REVERT: H 4 MET cc_start: 0.4604 (mmm) cc_final: 0.3839 (ttt) REVERT: L 33 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.4911 (tp) outliers start: 28 outliers final: 27 residues processed: 185 average time/residue: 0.4096 time to fit residues: 108.1802 Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 236 optimal weight: 0.0050 chunk 217 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.039 20469 Z= 0.582 Angle : 0.937 106.100 27807 Z= 0.407 Chirality : 0.045 0.380 3378 Planarity : 0.005 0.076 3429 Dihedral : 11.670 92.411 4370 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 1.32 % Allowed : 14.52 % Favored : 84.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2373 helix: 1.86 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 801 loop : -1.00 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.003 0.001 HIS C 374 PHE 0.044 0.002 PHE G 100H TYR 0.013 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8023 (tt0) cc_final: 0.7675 (tt0) REVERT: C 268 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6637 (pm20) REVERT: E 268 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6760 (pm20) REVERT: E 426 MET cc_start: 0.7368 (tpp) cc_final: 0.7129 (tpt) REVERT: H 4 MET cc_start: 0.4604 (mmm) cc_final: 0.3839 (ttt) REVERT: L 33 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.4911 (tp) outliers start: 28 outliers final: 27 residues processed: 185 average time/residue: 0.4275 time to fit residues: 112.9652 Evaluate side-chains 195 residues out of total 2121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 165 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.203880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.132185 restraints weight = 20688.380| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.36 r_work: 0.3077 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.039 20469 Z= 0.582 Angle : 0.937 106.100 27807 Z= 0.407 Chirality : 0.045 0.380 3378 Planarity : 0.005 0.076 3429 Dihedral : 11.670 92.411 4370 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 1.32 % Allowed : 14.52 % Favored : 84.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2373 helix: 1.86 (0.28), residues: 399 sheet: 0.19 (0.18), residues: 801 loop : -1.00 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.003 0.001 HIS C 374 PHE 0.044 0.002 PHE G 100H TYR 0.013 0.001 TYR C 173 ARG 0.004 0.000 ARG A 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4158.48 seconds wall clock time: 75 minutes 21.55 seconds (4521.55 seconds total)