Starting phenix.real_space_refine on Sat Sep 28 20:02:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orp_20177/09_2024/6orp_20177.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orp_20177/09_2024/6orp_20177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orp_20177/09_2024/6orp_20177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orp_20177/09_2024/6orp_20177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orp_20177/09_2024/6orp_20177.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orp_20177/09_2024/6orp_20177.cif" } resolution = 4.4 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= -0.002 sd= 0.204 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 114 5.16 5 C 12487 2.51 5 N 3317 2.21 5 O 4054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 19972 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "I" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "J" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "K" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" 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: "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: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "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: 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: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 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: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "G" 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: "I" 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: 11.83, per 1000 atoms: 0.59 Number of scatterers: 19972 At special positions: 0 Unit cell: (139.292, 133.548, 150.78, 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 114 16.00 O 4054 8.00 N 3317 7.00 C 12487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS B 501 " distance=2.05 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.05 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.07 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.05 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.06 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.05 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.02 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.09 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.09 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " 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 ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA b 3 " - " MAN b 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA j 3 " - " MAN j 5 " 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 P 2 " - " BMA P 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " 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 g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 601 " - " ASN B 88 " " NAG B 614 " - " ASN B 295 " " NAG B 620 " - " ASN B 339 " " NAG B 621 " - " ASN B 355 " " NAG C 703 " - " ASN C 618 " " NAG C 704 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 615 " - " ASN G 295 " " NAG G 620 " - " ASN G 339 " " NAG G 621 " - " ASN G 355 " " NAG G 622 " - " ASN G 392 " " NAG G 627 " - " ASN G 448 " " NAG I 601 " - " ASN I 88 " " NAG I 619 " - " ASN I 295 " " NAG I 625 " - " ASN I 339 " " NAG I 626 " - " ASN I 355 " " NAG I 631 " - " ASN I 448 " " NAG M 1 " - " ASN B 160 " " NAG N 1 " - " ASN B 197 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 262 " " NAG Q 1 " - " ASN B 301 " " NAG R 1 " - " ASN B 332 " " NAG S 1 " - " ASN B 386 " " NAG T 1 " - " ASN B 448 " " NAG U 1 " - " ASN B 392 " " NAG V 1 " - " ASN B 276 " " NAG W 1 " - " ASN C 611 " " NAG X 1 " - " ASN G 88 " " NAG Y 1 " - " ASN G 160 " " NAG Z 1 " - " ASN G 197 " " NAG a 1 " - " ASN G 234 " " NAG b 1 " - " ASN G 262 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 279 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN I 160 " " NAG h 1 " - " ASN I 197 " " NAG i 1 " - " ASN I 234 " " NAG j 1 " - " ASN I 262 " " NAG k 1 " - " ASN I 279 " " NAG l 1 " - " ASN I 301 " " NAG m 1 " - " ASN I 332 " " NAG n 1 " - " ASN I 386 " " NAG o 1 " - " ASN I 392 " Time building additional restraints: 5.55 Conformation dependent library (CDL) restraints added in 2.2 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4422 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 43 sheets defined 16.8% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 543 removed outlier: 3.666A pdb=" N ALA A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.579A pdb=" N VAL A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.611A pdb=" N ILE A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 removed outlier: 3.502A pdb=" N ASP A 632 " --> pdb=" O TRP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 648 removed outlier: 3.696A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.782A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.602A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 removed outlier: 4.208A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 546 removed outlier: 3.695A pdb=" N ALA C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 546 " --> pdb=" O ARG C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.641A pdb=" N VAL C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 632 removed outlier: 3.618A pdb=" N ASP C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 649 removed outlier: 4.967A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 661 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.760A pdb=" N SER D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER D 32 " --> pdb=" O ILE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'E' and resid 26 through 29 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.764A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 595 removed outlier: 4.415A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.595A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 632 Processing helix chain 'F' and resid 638 through 648 removed outlier: 4.451A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 661 Processing helix chain 'G' and resid 99 through 116 removed outlier: 3.641A pdb=" N GLN G 103 " --> pdb=" O ASN G 99 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.634A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.722A pdb=" N ARG G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 476 through 481' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.761A pdb=" N SER H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.618A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 351 through 353 No H-bonds generated for 'chain 'I' and resid 351 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.557A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 481 removed outlier: 3.830A pdb=" N ARG I 480 " --> pdb=" O ARG I 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.760A pdb=" N SER J 31 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER J 32 " --> pdb=" O ILE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'K' and resid 26 through 29 Processing helix chain 'L' and resid 26 through 29 Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 46 removed outlier: 9.153A pdb=" N ILE B 491 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TRP B 45 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N VAL B 489 " --> pdb=" O TRP B 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 76 removed outlier: 4.360A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 176 removed outlier: 3.734A pdb=" N VAL B 172 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 159 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS B 131 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 189 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU B 190 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.249A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.130A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.511A pdb=" N ILE B 271 " --> pdb=" O GLN B 287 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 452 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.903A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 334 removed outlier: 3.785A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 8 removed outlier: 3.621A pdb=" N GLY D 8 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR D 21 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 17 through 18 removed outlier: 3.884A pdb=" N THR D 69 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 49 removed outlier: 4.514A pdb=" N TRP D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 19 through 24 removed outlier: 4.042A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 90 through 92 removed outlier: 3.644A pdb=" N ALA E 95B" --> pdb=" O ASP E 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 35 through 46 removed outlier: 3.540A pdb=" N GLY G 495 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N ILE G 491 " --> pdb=" O PRO G 43 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TRP G 45 " --> pdb=" O VAL G 489 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N VAL G 489 " --> pdb=" O TRP G 45 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 75 through 76 removed outlier: 4.458A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 92 through 94 removed outlier: 4.142A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 169 through 176 removed outlier: 3.923A pdb=" N VAL G 172 " --> pdb=" O PHE G 159 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE G 159 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS G 131 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.269A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 256 through 257 Processing sheet with id=AC2, first strand: chain 'G' and resid 259 through 260 removed outlier: 3.728A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 259 through 260 removed outlier: 6.589A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 383 through 385 removed outlier: 3.756A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 383 through 385 removed outlier: 3.756A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 304 through 307 removed outlier: 3.576A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.620A pdb=" N GLY H 8 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR H 21 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 17 through 18 removed outlier: 3.884A pdb=" N THR H 69 " --> pdb=" O LYS H 82 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 47 through 49 removed outlier: 4.514A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 35 through 46 removed outlier: 9.239A pdb=" N ILE I 491 " --> pdb=" O PRO I 43 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N TRP I 45 " --> pdb=" O VAL I 489 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N VAL I 489 " --> pdb=" O TRP I 45 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 53 through 55 removed outlier: 5.853A pdb=" N ILE I 215 " --> pdb=" O GLY I 250 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY I 250 " --> pdb=" O ILE I 215 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR I 217 " --> pdb=" O THR I 248 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 92 through 94 removed outlier: 4.139A pdb=" N GLY I 237 " --> pdb=" O PHE I 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 169 through 176 removed outlier: 3.840A pdb=" N PHE I 159 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS I 131 " --> pdb=" O LYS I 189 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 202 through 203 removed outlier: 5.852A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.823A pdb=" N ILE I 271 " --> pdb=" O GLN I 287 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 383 through 385 removed outlier: 3.673A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 383 through 385 removed outlier: 3.673A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR I 297 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 301 through 308 removed outlier: 7.656A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 6 through 8 removed outlier: 3.620A pdb=" N GLY J 8 " --> pdb=" O THR J 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR J 21 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 17 through 18 removed outlier: 3.884A pdb=" N THR J 69 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 47 through 49 removed outlier: 4.513A pdb=" N TRP J 37 " --> pdb=" O ILE J 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.042A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 90 through 92 removed outlier: 3.646A pdb=" N ALA K 95B" --> pdb=" O ASP K 92 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.042A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 90 through 92 removed outlier: 3.645A pdb=" N ALA L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.34 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3206 1.31 - 1.45: 6838 1.45 - 1.59: 10176 1.59 - 1.73: 1 1.73 - 1.87: 150 Bond restraints: 20371 Sorted by residual: bond pdb=" C4 NAG e 1 " pdb=" O4 NAG e 1 " ideal model delta sigma weight residual 1.409 1.524 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C7 NAG B 614 " pdb=" N2 NAG B 614 " ideal model delta sigma weight residual 1.346 1.243 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C1 NAG B 614 " pdb=" C2 NAG B 614 " ideal model delta sigma weight residual 1.532 1.434 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C2 NAG B 614 " pdb=" N2 NAG B 614 " ideal model delta sigma weight residual 1.439 1.342 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C3 NAG B 614 " pdb=" C4 NAG B 614 " ideal model delta sigma weight residual 1.524 1.432 0.092 2.00e-02 2.50e+03 2.12e+01 ... (remaining 20366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 27250 5.28 - 10.56: 362 10.56 - 15.84: 48 15.84 - 21.12: 10 21.12 - 26.40: 4 Bond angle restraints: 27674 Sorted by residual: angle pdb=" CA ASN G 448 " pdb=" C ASN G 448 " pdb=" O ASN G 448 " ideal model delta sigma weight residual 119.32 104.70 14.62 1.19e+00 7.06e-01 1.51e+02 angle pdb=" C ASN G 448 " pdb=" N ILE G 449 " pdb=" CA ILE G 449 " ideal model delta sigma weight residual 121.97 140.56 -18.59 1.80e+00 3.09e-01 1.07e+02 angle pdb=" O SER G 447 " pdb=" C SER G 447 " pdb=" N ASN G 448 " ideal model delta sigma weight residual 123.10 133.55 -10.45 1.15e+00 7.56e-01 8.26e+01 angle pdb=" C3 NAG C 704 " pdb=" C2 NAG C 704 " pdb=" N2 NAG C 704 " ideal model delta sigma weight residual 110.74 84.34 26.40 3.00e+00 1.11e-01 7.75e+01 angle pdb=" C1 NAG j 1 " pdb=" C2 NAG j 1 " pdb=" N2 NAG j 1 " ideal model delta sigma weight residual 110.79 88.76 22.03 3.00e+00 1.11e-01 5.39e+01 ... (remaining 27669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 12278 22.45 - 44.91: 814 44.91 - 67.36: 155 67.36 - 89.81: 105 89.81 - 112.26: 55 Dihedral angle restraints: 13407 sinusoidal: 6537 harmonic: 6870 Sorted by residual: dihedral pdb=" CB CYS F 605 " pdb=" SG CYS F 605 " pdb=" SG CYS I 501 " pdb=" CB CYS I 501 " ideal model delta sinusoidal sigma weight residual -86.00 2.89 -88.89 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CA GLN K 34 " pdb=" C GLN K 34 " pdb=" N TRP K 35 " pdb=" CA TRP K 35 " ideal model delta harmonic sigma weight residual 180.00 134.99 45.01 0 5.00e+00 4.00e-02 8.10e+01 dihedral pdb=" CA GLN L 34 " pdb=" C GLN L 34 " pdb=" N TRP L 35 " pdb=" CA TRP L 35 " ideal model delta harmonic sigma weight residual 180.00 135.03 44.97 0 5.00e+00 4.00e-02 8.09e+01 ... (remaining 13404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.241: 3307 0.241 - 0.483: 73 0.483 - 0.724: 5 0.724 - 0.965: 2 0.965 - 1.207: 4 Chirality restraints: 3391 Sorted by residual: chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.81 0.41 2.00e-02 2.50e+03 4.13e+02 chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-02 2.50e+03 2.63e+02 chirality pdb=" C1 NAG j 2 " pdb=" O4 NAG j 1 " pdb=" C2 NAG j 2 " pdb=" O5 NAG j 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.54e+02 ... (remaining 3388 not shown) Planarity restraints: 3440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 1 " -0.366 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG f 1 " 0.096 2.00e-02 2.50e+03 pdb=" C8 NAG f 1 " -0.192 2.00e-02 2.50e+03 pdb=" N2 NAG f 1 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG f 1 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 2 " 0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG U 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG U 2 " 0.100 2.00e-02 2.50e+03 pdb=" N2 NAG U 2 " -0.529 2.00e-02 2.50e+03 pdb=" O7 NAG U 2 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.336 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG j 1 " 0.120 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.499 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.104 2.00e-02 2.50e+03 ... (remaining 3437 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 15 2.21 - 2.88: 7971 2.88 - 3.56: 27575 3.56 - 4.23: 44211 4.23 - 4.90: 67651 Nonbonded interactions: 147423 Sorted by model distance: nonbonded pdb=" CE2 PHE B 391 " pdb=" CG PRO B 470 " model vdw 1.539 3.740 nonbonded pdb=" CE3 TRP G 96 " pdb=" OE2 GLU G 275 " model vdw 1.863 3.340 nonbonded pdb=" CE2 PHE B 391 " pdb=" CB PRO B 470 " model vdw 1.868 3.740 nonbonded pdb=" O4 NAG C 704 " pdb=" O6 NAG C 704 " model vdw 1.983 3.040 nonbonded pdb=" O4 NAG A 703 " pdb=" O6 NAG A 703 " model vdw 1.998 3.040 ... (remaining 147418 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' and (resid 518 through 664 or resid 701 through 702)) selection = chain 'C' selection = (chain 'F' and (resid 518 through 664 or resid 701 through 702)) } ncs_group { reference = chain 'B' selection = (chain 'G' and (resid 31 through 505 or resid 615 through 622)) selection = (chain 'I' and (resid 31 through 505 or resid 601 through 626)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'l' selection = chain 'n' selection = chain 'o' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'm' } ncs_group { reference = chain 'P' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 44.780 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 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 : 0.010 0.115 20371 Z= 0.593 Angle : 1.622 26.404 27674 Z= 0.817 Chirality : 0.099 1.207 3391 Planarity : 0.015 0.306 3389 Dihedral : 18.024 112.263 8895 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.43 % Allowed : 15.83 % Favored : 83.74 % Rotamer: Outliers : 1.05 % Allowed : 8.24 % Favored : 90.71 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 1.59 % 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: -4.88 (0.14), residues: 2343 helix: -3.44 (0.19), residues: 333 sheet: -2.48 (0.19), residues: 564 loop : -3.71 (0.14), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP H 100B HIS 0.021 0.003 HIS F 585 PHE 0.033 0.004 PHE B 320 TYR 0.073 0.004 TYR B 173 ARG 0.007 0.001 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 896 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 LEU cc_start: 0.8845 (mt) cc_final: 0.8627 (mt) REVERT: A 534 SER cc_start: 0.8967 (p) cc_final: 0.8602 (p) REVERT: A 543 ASN cc_start: 0.8175 (t0) cc_final: 0.7760 (t0) REVERT: A 624 ASP cc_start: 0.8398 (m-30) cc_final: 0.8198 (m-30) REVERT: B 97 LYS cc_start: 0.8313 (mmtp) cc_final: 0.8067 (mmmm) REVERT: B 116 LEU cc_start: 0.7173 (pp) cc_final: 0.6711 (pp) REVERT: B 131 CYS cc_start: 0.5986 (t) cc_final: 0.5697 (t) REVERT: B 150 MET cc_start: 0.7943 (mpp) cc_final: 0.7682 (mpp) REVERT: B 181 VAL cc_start: 0.7815 (t) cc_final: 0.7579 (t) REVERT: B 265 LEU cc_start: 0.8160 (mt) cc_final: 0.7826 (mm) REVERT: B 269 GLU cc_start: 0.8504 (tp30) cc_final: 0.8261 (tp30) REVERT: B 289 ASN cc_start: 0.8274 (p0) cc_final: 0.8045 (p0) REVERT: B 307 ILE cc_start: 0.7410 (mm) cc_final: 0.7121 (tp) REVERT: B 474 ASP cc_start: 0.7988 (t70) cc_final: 0.6689 (t0) REVERT: B 485 LYS cc_start: 0.6351 (ptpt) cc_final: 0.6107 (ptpp) REVERT: C 534 SER cc_start: 0.8972 (p) cc_final: 0.8582 (p) REVERT: C 543 ASN cc_start: 0.7901 (t0) cc_final: 0.7693 (t0) REVERT: C 583 VAL cc_start: 0.6947 (m) cc_final: 0.6678 (m) REVERT: C 624 ASP cc_start: 0.8130 (m-30) cc_final: 0.7793 (m-30) REVERT: C 658 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8272 (tp-100) REVERT: E 58 LEU cc_start: 0.7936 (tp) cc_final: 0.7497 (tp) REVERT: E 60 ASP cc_start: 0.6980 (t0) cc_final: 0.6147 (t0) REVERT: E 92 ASP cc_start: 0.7970 (t0) cc_final: 0.7703 (m-30) REVERT: F 522 PHE cc_start: 0.7390 (t80) cc_final: 0.6343 (t80) REVERT: F 534 SER cc_start: 0.8840 (p) cc_final: 0.8476 (p) REVERT: F 543 ASN cc_start: 0.7950 (t0) cc_final: 0.7699 (t0) REVERT: F 590 GLN cc_start: 0.8423 (tp-100) cc_final: 0.8180 (tm-30) REVERT: F 624 ASP cc_start: 0.8025 (m-30) cc_final: 0.7740 (m-30) REVERT: G 82 GLN cc_start: 0.8764 (mm-40) cc_final: 0.7947 (mp10) REVERT: G 94 ASN cc_start: 0.7961 (t0) cc_final: 0.7539 (t0) REVERT: G 98 ASN cc_start: 0.8262 (t0) cc_final: 0.8036 (t0) REVERT: G 171 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7575 (mtmt) REVERT: G 203 GLN cc_start: 0.7278 (pp30) cc_final: 0.6735 (pp30) REVERT: G 269 GLU cc_start: 0.8300 (tp30) cc_final: 0.7880 (tp30) REVERT: G 289 ASN cc_start: 0.8341 (p0) cc_final: 0.7919 (p0) REVERT: G 320 PHE cc_start: 0.8099 (t80) cc_final: 0.7384 (t80) REVERT: G 321 ASP cc_start: 0.7970 (m-30) cc_final: 0.7728 (m-30) REVERT: G 369 LEU cc_start: 0.8293 (pp) cc_final: 0.8021 (mm) REVERT: G 426 MET cc_start: 0.7626 (ptt) cc_final: 0.7313 (ptm) REVERT: G 474 ASP cc_start: 0.7070 (t70) cc_final: 0.6544 (t70) REVERT: G 478 ASN cc_start: 0.6956 (m110) cc_final: 0.6553 (m110) REVERT: G 488 VAL cc_start: 0.5941 (p) cc_final: 0.5305 (p) REVERT: H 57 ASN cc_start: 0.6348 (t0) cc_final: 0.6065 (t0) REVERT: I 50 THR cc_start: 0.9334 (p) cc_final: 0.8960 (p) REVERT: I 53 PHE cc_start: 0.6691 (p90) cc_final: 0.6441 (p90) REVERT: I 87 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6670 (tm-30) REVERT: I 97 LYS cc_start: 0.8596 (mmtp) cc_final: 0.8267 (mmmm) REVERT: I 171 LYS cc_start: 0.8170 (pmmt) cc_final: 0.7560 (ptmt) REVERT: I 172 VAL cc_start: 0.8136 (p) cc_final: 0.7846 (p) REVERT: I 261 LEU cc_start: 0.7152 (tp) cc_final: 0.6907 (tp) REVERT: I 269 GLU cc_start: 0.8282 (tp30) cc_final: 0.8068 (tp30) REVERT: I 278 THR cc_start: 0.9055 (m) cc_final: 0.8835 (t) REVERT: I 289 ASN cc_start: 0.8238 (p0) cc_final: 0.7675 (p0) REVERT: I 308 ARG cc_start: 0.7783 (mpp80) cc_final: 0.7350 (mtm-85) REVERT: I 383 PHE cc_start: 0.6136 (m-10) cc_final: 0.5809 (m-10) REVERT: I 443 ILE cc_start: 0.8020 (mm) cc_final: 0.7790 (mp) REVERT: J 9 PRO cc_start: 0.8372 (Cg_endo) cc_final: 0.8110 (Cg_exo) REVERT: J 78 GLN cc_start: 0.7794 (mp10) cc_final: 0.7460 (mp10) REVERT: J 91 TYR cc_start: 0.7187 (m-80) cc_final: 0.6972 (m-10) REVERT: K 22 SER cc_start: 0.9111 (m) cc_final: 0.8885 (t) REVERT: K 58 LEU cc_start: 0.7898 (tp) cc_final: 0.7640 (tp) REVERT: K 60 ASP cc_start: 0.6305 (t0) cc_final: 0.5119 (t0) REVERT: K 92 ASP cc_start: 0.8340 (t0) cc_final: 0.8103 (m-30) REVERT: L 34 GLN cc_start: 0.7034 (pp30) cc_final: 0.6795 (pp30) REVERT: L 58 LEU cc_start: 0.7707 (tp) cc_final: 0.7460 (tp) REVERT: L 60 ASP cc_start: 0.7037 (t0) cc_final: 0.6207 (t0) REVERT: L 92 ASP cc_start: 0.8116 (t0) cc_final: 0.7789 (m-30) outliers start: 22 outliers final: 9 residues processed: 909 average time/residue: 0.3080 time to fit residues: 424.7243 Evaluate side-chains 557 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 548 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.1980 chunk 177 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 136 optimal weight: 0.0770 chunk 212 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN A 651 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN B 258 GLN C 651 ASN C 656 ASN F 651 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 ASN G 156 GLN G 170 GLN G 425 ASN H 78 GLN I 137 ASN I 156 GLN I 170 GLN I 302 ASN I 425 ASN L 38 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20371 Z= 0.241 Angle : 1.013 12.180 27674 Z= 0.478 Chirality : 0.061 0.640 3391 Planarity : 0.006 0.059 3389 Dihedral : 15.465 88.153 4566 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.31 % Favored : 88.60 % Rotamer: Outliers : 0.34 % Allowed : 5.70 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.62 % 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: -4.30 (0.15), residues: 2343 helix: -2.51 (0.23), residues: 336 sheet: -1.69 (0.23), residues: 423 loop : -3.53 (0.13), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 100B HIS 0.007 0.001 HIS G 374 PHE 0.039 0.002 PHE K 31 TYR 0.033 0.002 TYR I 173 ARG 0.007 0.001 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 765 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8427 (t0) cc_final: 0.8072 (t0) REVERT: A 661 LEU cc_start: 0.8664 (tp) cc_final: 0.8418 (tt) REVERT: B 97 LYS cc_start: 0.8371 (mmtp) cc_final: 0.8140 (mmmm) REVERT: B 106 GLU cc_start: 0.8265 (pt0) cc_final: 0.7902 (tm-30) REVERT: B 122 LEU cc_start: 0.5506 (tp) cc_final: 0.5303 (tt) REVERT: B 181 VAL cc_start: 0.7520 (t) cc_final: 0.7170 (t) REVERT: B 265 LEU cc_start: 0.8319 (mt) cc_final: 0.7853 (mm) REVERT: B 270 VAL cc_start: 0.9520 (m) cc_final: 0.9318 (t) REVERT: B 279 ASN cc_start: 0.6371 (t0) cc_final: 0.6050 (t0) REVERT: B 315 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7826 (mp10) REVERT: B 321 ASP cc_start: 0.8844 (m-30) cc_final: 0.8495 (m-30) REVERT: B 474 ASP cc_start: 0.7647 (t70) cc_final: 0.6633 (t0) REVERT: B 475 MET cc_start: 0.7078 (mmm) cc_final: 0.6762 (mmm) REVERT: B 492 GLU cc_start: 0.8411 (tp30) cc_final: 0.7364 (tm-30) REVERT: C 588 ARG cc_start: 0.7825 (ttt90) cc_final: 0.7597 (ttt180) REVERT: C 603 ILE cc_start: 0.6885 (pt) cc_final: 0.6456 (pt) REVERT: C 620 SER cc_start: 0.8213 (m) cc_final: 0.7961 (p) REVERT: C 658 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8094 (tp-100) REVERT: D 36 SER cc_start: 0.9140 (t) cc_final: 0.8920 (t) REVERT: D 48 TRP cc_start: 0.8297 (t60) cc_final: 0.7773 (t60) REVERT: D 57 ASN cc_start: 0.6816 (t0) cc_final: 0.6557 (t0) REVERT: D 58 THR cc_start: 0.8583 (p) cc_final: 0.8382 (m) REVERT: E 49 TYR cc_start: 0.7495 (t80) cc_final: 0.7234 (t80) REVERT: E 54 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8032 (mmp80) REVERT: E 60 ASP cc_start: 0.5806 (t0) cc_final: 0.4245 (t0) REVERT: E 92 ASP cc_start: 0.7904 (t0) cc_final: 0.7578 (m-30) REVERT: F 522 PHE cc_start: 0.6810 (t80) cc_final: 0.6196 (t80) REVERT: F 543 ASN cc_start: 0.7956 (t0) cc_final: 0.7644 (t0) REVERT: G 49 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8178 (tp30) REVERT: G 50 THR cc_start: 0.9258 (p) cc_final: 0.8937 (p) REVERT: G 82 GLN cc_start: 0.8764 (mm-40) cc_final: 0.7961 (mp10) REVERT: G 94 ASN cc_start: 0.7728 (t0) cc_final: 0.7443 (t0) REVERT: G 95 MET cc_start: 0.9450 (ptm) cc_final: 0.9175 (ptm) REVERT: G 156 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: G 203 GLN cc_start: 0.7550 (pp30) cc_final: 0.6526 (pp30) REVERT: G 226 LEU cc_start: 0.6962 (pp) cc_final: 0.6760 (pp) REVERT: G 239 CYS cc_start: 0.5158 (t) cc_final: 0.4890 (t) REVERT: G 269 GLU cc_start: 0.8361 (tp30) cc_final: 0.7783 (tp30) REVERT: G 289 ASN cc_start: 0.8500 (p0) cc_final: 0.8190 (p0) REVERT: G 325 ASP cc_start: 0.7883 (p0) cc_final: 0.7471 (p0) REVERT: G 425 ASN cc_start: 0.7456 (OUTLIER) cc_final: 0.6863 (p0) REVERT: G 426 MET cc_start: 0.7691 (ptt) cc_final: 0.7442 (ptt) REVERT: G 453 ILE cc_start: 0.7342 (pt) cc_final: 0.6940 (pt) REVERT: G 492 GLU cc_start: 0.8307 (tp30) cc_final: 0.7918 (tp30) REVERT: G 494 LEU cc_start: 0.8665 (tt) cc_final: 0.8435 (tt) REVERT: H 36 SER cc_start: 0.8848 (t) cc_final: 0.8517 (t) REVERT: H 91 TYR cc_start: 0.7752 (m-10) cc_final: 0.7315 (m-10) REVERT: I 50 THR cc_start: 0.9186 (p) cc_final: 0.8904 (p) REVERT: I 53 PHE cc_start: 0.6813 (p90) cc_final: 0.6505 (p90) REVERT: I 87 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6829 (tm-30) REVERT: I 95 MET cc_start: 0.9461 (ptm) cc_final: 0.9179 (ptm) REVERT: I 97 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8275 (mmmm) REVERT: I 156 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: I 180 ASP cc_start: 0.8116 (m-30) cc_final: 0.7649 (m-30) REVERT: I 269 GLU cc_start: 0.8241 (tp30) cc_final: 0.7684 (tp30) REVERT: I 289 ASN cc_start: 0.8280 (p0) cc_final: 0.7883 (p0) REVERT: I 308 ARG cc_start: 0.7539 (mpp80) cc_final: 0.7164 (mtm-85) REVERT: I 368 ASP cc_start: 0.7449 (t70) cc_final: 0.7230 (t70) REVERT: I 426 MET cc_start: 0.8118 (ptt) cc_final: 0.7664 (ptm) REVERT: I 427 TRP cc_start: 0.8216 (m100) cc_final: 0.7231 (m100) REVERT: I 485 LYS cc_start: 0.6933 (ptpt) cc_final: 0.6710 (ptpt) REVERT: J 57 ASN cc_start: 0.6509 (t0) cc_final: 0.6303 (t0) REVERT: J 96 ASP cc_start: 0.8746 (m-30) cc_final: 0.8520 (m-30) REVERT: K 54 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.8027 (mmm-85) REVERT: K 60 ASP cc_start: 0.5780 (t0) cc_final: 0.4949 (t0) REVERT: K 92 ASP cc_start: 0.8343 (t0) cc_final: 0.7996 (m-30) REVERT: L 54 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.8184 (mmm-85) REVERT: L 60 ASP cc_start: 0.6412 (t0) cc_final: 0.5832 (t0) REVERT: L 92 ASP cc_start: 0.7972 (t0) cc_final: 0.7672 (m-30) outliers start: 7 outliers final: 0 residues processed: 767 average time/residue: 0.2913 time to fit residues: 347.4148 Evaluate side-chains 564 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 561 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.4980 chunk 65 optimal weight: 0.0170 chunk 176 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN B 156 GLN D 61 ASN G 156 GLN H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 425 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20371 Z= 0.221 Angle : 0.929 14.578 27674 Z= 0.439 Chirality : 0.058 0.561 3391 Planarity : 0.005 0.057 3389 Dihedral : 13.421 88.391 4566 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.12 % Favored : 87.79 % Rotamer: Outliers : 0.38 % Allowed : 4.50 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -3.96 (0.15), residues: 2343 helix: -2.06 (0.24), residues: 336 sheet: -1.47 (0.22), residues: 510 loop : -3.41 (0.14), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 596 HIS 0.005 0.001 HIS G 374 PHE 0.020 0.002 PHE I 320 TYR 0.035 0.002 TYR H 92 ARG 0.006 0.001 ARG C 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 670 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 THR cc_start: 0.7911 (p) cc_final: 0.7546 (p) REVERT: A 543 ASN cc_start: 0.8448 (t0) cc_final: 0.8062 (t0) REVERT: A 588 ARG cc_start: 0.7792 (ttt90) cc_final: 0.7478 (ttt180) REVERT: A 630 GLN cc_start: 0.8133 (mp10) cc_final: 0.7858 (mp10) REVERT: B 97 LYS cc_start: 0.8453 (mmtp) cc_final: 0.8182 (mmmm) REVERT: B 106 GLU cc_start: 0.8130 (pt0) cc_final: 0.7704 (tm-30) REVERT: B 122 LEU cc_start: 0.6918 (tp) cc_final: 0.6563 (tt) REVERT: B 171 LYS cc_start: 0.7684 (ptpp) cc_final: 0.7398 (ptmm) REVERT: B 181 VAL cc_start: 0.7323 (t) cc_final: 0.6743 (t) REVERT: B 265 LEU cc_start: 0.8220 (mt) cc_final: 0.7682 (mm) REVERT: B 279 ASN cc_start: 0.6452 (t0) cc_final: 0.6046 (t0) REVERT: B 368 ASP cc_start: 0.6431 (t0) cc_final: 0.6194 (t70) REVERT: B 426 MET cc_start: 0.8644 (ptt) cc_final: 0.8015 (ptm) REVERT: B 474 ASP cc_start: 0.7629 (t70) cc_final: 0.6480 (t70) REVERT: B 475 MET cc_start: 0.7028 (mmm) cc_final: 0.5963 (tmm) REVERT: B 492 GLU cc_start: 0.8330 (tp30) cc_final: 0.8060 (tt0) REVERT: C 530 MET cc_start: 0.8818 (ttm) cc_final: 0.8557 (mmm) REVERT: C 630 GLN cc_start: 0.8318 (mp10) cc_final: 0.7979 (mp10) REVERT: C 658 GLN cc_start: 0.8409 (tp-100) cc_final: 0.8119 (tp40) REVERT: D 22 CYS cc_start: 0.7661 (t) cc_final: 0.7273 (t) REVERT: D 48 TRP cc_start: 0.8296 (t60) cc_final: 0.7834 (t60) REVERT: D 52 ILE cc_start: 0.8405 (tp) cc_final: 0.7793 (tp) REVERT: D 57 ASN cc_start: 0.7118 (t0) cc_final: 0.6807 (t0) REVERT: E 11 VAL cc_start: 0.6315 (t) cc_final: 0.6102 (t) REVERT: E 85 ASP cc_start: 0.8390 (m-30) cc_final: 0.8163 (m-30) REVERT: E 92 ASP cc_start: 0.7950 (t0) cc_final: 0.7613 (m-30) REVERT: F 522 PHE cc_start: 0.7014 (t80) cc_final: 0.6610 (t80) REVERT: F 523 LEU cc_start: 0.8537 (mt) cc_final: 0.8333 (mt) REVERT: F 543 ASN cc_start: 0.8112 (t0) cc_final: 0.7768 (t0) REVERT: F 638 TYR cc_start: 0.7995 (m-10) cc_final: 0.7769 (m-10) REVERT: G 49 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7903 (tp30) REVERT: G 82 GLN cc_start: 0.8772 (mm-40) cc_final: 0.7988 (mp10) REVERT: G 92 GLU cc_start: 0.6813 (pp20) cc_final: 0.6399 (pp20) REVERT: G 95 MET cc_start: 0.9425 (ptm) cc_final: 0.9067 (ptm) REVERT: G 112 TRP cc_start: 0.7596 (t-100) cc_final: 0.7165 (t-100) REVERT: G 156 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6500 (pm20) REVERT: G 157 CYS cc_start: 0.7646 (m) cc_final: 0.7299 (m) REVERT: G 164 GLU cc_start: 0.9050 (pp20) cc_final: 0.8636 (pp20) REVERT: G 181 VAL cc_start: 0.7929 (t) cc_final: 0.7713 (t) REVERT: G 225 ILE cc_start: 0.7168 (mm) cc_final: 0.6959 (mm) REVERT: G 289 ASN cc_start: 0.8584 (p0) cc_final: 0.8351 (p0) REVERT: G 356 ASN cc_start: 0.9130 (t0) cc_final: 0.8852 (p0) REVERT: G 426 MET cc_start: 0.7822 (ptt) cc_final: 0.7598 (ptt) REVERT: G 479 TRP cc_start: 0.8450 (m-90) cc_final: 0.7635 (m-90) REVERT: G 492 GLU cc_start: 0.8355 (tp30) cc_final: 0.8128 (tp30) REVERT: H 36 SER cc_start: 0.8942 (t) cc_final: 0.8664 (t) REVERT: H 57 ASN cc_start: 0.6608 (t0) cc_final: 0.6395 (t0) REVERT: H 67 ARG cc_start: 0.6550 (mmm160) cc_final: 0.5580 (mmm160) REVERT: I 50 THR cc_start: 0.9123 (p) cc_final: 0.8858 (p) REVERT: I 53 PHE cc_start: 0.6680 (p90) cc_final: 0.6460 (p90) REVERT: I 97 LYS cc_start: 0.8587 (mmtp) cc_final: 0.8248 (mmmm) REVERT: I 112 TRP cc_start: 0.7323 (t-100) cc_final: 0.7088 (t-100) REVERT: I 156 GLN cc_start: 0.7566 (pp30) cc_final: 0.6975 (pm20) REVERT: I 170 GLN cc_start: 0.5718 (tt0) cc_final: 0.5517 (tt0) REVERT: I 180 ASP cc_start: 0.7888 (m-30) cc_final: 0.7307 (m-30) REVERT: I 211 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7507 (tm-30) REVERT: I 289 ASN cc_start: 0.8249 (p0) cc_final: 0.8003 (p0) REVERT: I 307 ILE cc_start: 0.7399 (mm) cc_final: 0.7049 (tp) REVERT: I 308 ARG cc_start: 0.7561 (mpp80) cc_final: 0.7232 (mtm-85) REVERT: I 368 ASP cc_start: 0.7264 (t70) cc_final: 0.6884 (t70) REVERT: I 426 MET cc_start: 0.8005 (ptt) cc_final: 0.7073 (ptm) REVERT: J 40 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7688 (tm-30) REVERT: J 57 ASN cc_start: 0.6637 (t0) cc_final: 0.6378 (t0) REVERT: K 60 ASP cc_start: 0.5885 (t0) cc_final: 0.5268 (t0) REVERT: K 92 ASP cc_start: 0.8330 (t0) cc_final: 0.7977 (m-30) REVERT: L 92 ASP cc_start: 0.7921 (t0) cc_final: 0.7604 (m-30) outliers start: 8 outliers final: 2 residues processed: 674 average time/residue: 0.2905 time to fit residues: 304.9635 Evaluate side-chains 553 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 550 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 213 optimal weight: 8.9990 chunk 226 optimal weight: 9.9990 chunk 111 optimal weight: 0.0010 chunk 202 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN I 156 GLN I 203 GLN I 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20371 Z= 0.226 Angle : 0.890 11.408 27674 Z= 0.419 Chirality : 0.055 0.490 3391 Planarity : 0.005 0.066 3389 Dihedral : 12.183 87.082 4566 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.51 % Favored : 87.41 % Rotamer: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.40 % 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: -3.85 (0.16), residues: 2343 helix: -1.85 (0.24), residues: 354 sheet: -1.53 (0.22), residues: 480 loop : -3.30 (0.14), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 34 HIS 0.006 0.001 HIS I 374 PHE 0.020 0.002 PHE I 320 TYR 0.035 0.002 TYR G 173 ARG 0.006 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 666 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8568 (t0) cc_final: 0.8208 (t0) REVERT: A 620 SER cc_start: 0.7995 (p) cc_final: 0.7742 (p) REVERT: A 630 GLN cc_start: 0.8177 (mp10) cc_final: 0.7813 (mp10) REVERT: B 49 GLU cc_start: 0.8596 (mp0) cc_final: 0.8199 (mp0) REVERT: B 92 GLU cc_start: 0.4491 (pp20) cc_final: 0.4197 (pp20) REVERT: B 96 TRP cc_start: 0.9408 (m100) cc_final: 0.8850 (m100) REVERT: B 106 GLU cc_start: 0.8017 (pt0) cc_final: 0.7797 (tm-30) REVERT: B 150 MET cc_start: 0.8707 (mmp) cc_final: 0.8472 (mpp) REVERT: B 256 SER cc_start: 0.6749 (t) cc_final: 0.6438 (t) REVERT: B 265 LEU cc_start: 0.8237 (mt) cc_final: 0.7711 (mm) REVERT: B 279 ASN cc_start: 0.6936 (t0) cc_final: 0.6531 (t0) REVERT: B 315 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7217 (mp10) REVERT: B 412 ASP cc_start: 0.7611 (m-30) cc_final: 0.7405 (t70) REVERT: B 474 ASP cc_start: 0.7699 (t70) cc_final: 0.6455 (t70) REVERT: B 475 MET cc_start: 0.6612 (mmm) cc_final: 0.6050 (mmm) REVERT: B 492 GLU cc_start: 0.8231 (tp30) cc_final: 0.7943 (tt0) REVERT: C 543 ASN cc_start: 0.7865 (t0) cc_final: 0.7663 (t0) REVERT: C 620 SER cc_start: 0.8435 (m) cc_final: 0.8213 (p) REVERT: C 630 GLN cc_start: 0.8297 (mp10) cc_final: 0.8056 (mp10) REVERT: C 658 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7921 (tp40) REVERT: D 22 CYS cc_start: 0.7974 (t) cc_final: 0.7556 (t) REVERT: D 47 GLU cc_start: 0.7650 (tp30) cc_final: 0.7379 (tp30) REVERT: D 52 ILE cc_start: 0.8128 (tp) cc_final: 0.7674 (tp) REVERT: D 57 ASN cc_start: 0.7236 (t0) cc_final: 0.6840 (t0) REVERT: E 31 PHE cc_start: 0.3690 (t80) cc_final: 0.3390 (t80) REVERT: E 85 ASP cc_start: 0.8483 (m-30) cc_final: 0.8264 (m-30) REVERT: E 92 ASP cc_start: 0.7973 (t0) cc_final: 0.7627 (m-30) REVERT: F 543 ASN cc_start: 0.8252 (t0) cc_final: 0.7920 (t0) REVERT: F 630 GLN cc_start: 0.7844 (mp10) cc_final: 0.7639 (mp10) REVERT: F 638 TYR cc_start: 0.8141 (m-10) cc_final: 0.7874 (m-10) REVERT: F 664 ASP cc_start: 0.6917 (p0) cc_final: 0.6702 (p0) REVERT: G 82 GLN cc_start: 0.8604 (mm-40) cc_final: 0.7838 (mp10) REVERT: G 92 GLU cc_start: 0.6859 (pp20) cc_final: 0.6512 (pp20) REVERT: G 94 ASN cc_start: 0.7925 (t0) cc_final: 0.7547 (t0) REVERT: G 95 MET cc_start: 0.9383 (ptm) cc_final: 0.9123 (ptm) REVERT: G 98 ASN cc_start: 0.8679 (t0) cc_final: 0.8452 (t0) REVERT: G 164 GLU cc_start: 0.8937 (pp20) cc_final: 0.8455 (pp20) REVERT: G 180 ASP cc_start: 0.7851 (m-30) cc_final: 0.7415 (m-30) REVERT: G 195 ASN cc_start: 0.7506 (t0) cc_final: 0.7281 (t0) REVERT: G 269 GLU cc_start: 0.8226 (tp30) cc_final: 0.7795 (tp30) REVERT: G 321 ASP cc_start: 0.8510 (m-30) cc_final: 0.8279 (m-30) REVERT: G 328 MET cc_start: 0.6307 (pmm) cc_final: 0.6033 (pmm) REVERT: G 350 ARG cc_start: 0.8432 (mtt180) cc_final: 0.8121 (tpt-90) REVERT: G 356 ASN cc_start: 0.9126 (t0) cc_final: 0.8732 (p0) REVERT: G 492 GLU cc_start: 0.8324 (tp30) cc_final: 0.8047 (tp30) REVERT: G 499 THR cc_start: 0.7036 (t) cc_final: 0.6810 (t) REVERT: H 18 LEU cc_start: 0.7267 (tt) cc_final: 0.7022 (tt) REVERT: H 22 CYS cc_start: 0.8668 (t) cc_final: 0.8407 (t) REVERT: H 57 ASN cc_start: 0.6566 (t0) cc_final: 0.6349 (t0) REVERT: H 79 PHE cc_start: 0.8239 (p90) cc_final: 0.7990 (p90) REVERT: I 50 THR cc_start: 0.9092 (p) cc_final: 0.8765 (p) REVERT: I 53 PHE cc_start: 0.6787 (p90) cc_final: 0.6510 (p90) REVERT: I 71 THR cc_start: 0.8821 (m) cc_final: 0.8608 (m) REVERT: I 97 LYS cc_start: 0.8606 (mmtp) cc_final: 0.8247 (mmmm) REVERT: I 114 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8749 (tm-30) REVERT: I 129 LEU cc_start: 0.7446 (mm) cc_final: 0.7236 (mm) REVERT: I 180 ASP cc_start: 0.7587 (m-30) cc_final: 0.7363 (m-30) REVERT: I 211 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7481 (tm-30) REVERT: I 289 ASN cc_start: 0.8286 (p0) cc_final: 0.7892 (p0) REVERT: I 307 ILE cc_start: 0.7448 (mm) cc_final: 0.7165 (tp) REVERT: I 308 ARG cc_start: 0.7600 (mpp80) cc_final: 0.7278 (mtm-85) REVERT: I 320 PHE cc_start: 0.7161 (t80) cc_final: 0.6489 (t80) REVERT: I 425 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.6798 (p0) REVERT: J 57 ASN cc_start: 0.6703 (t0) cc_final: 0.6394 (t0) REVERT: J 61 ASN cc_start: 0.6647 (t0) cc_final: 0.6258 (t0) REVERT: K 60 ASP cc_start: 0.5983 (t0) cc_final: 0.5500 (t0) REVERT: K 92 ASP cc_start: 0.8317 (t0) cc_final: 0.7975 (m-30) REVERT: L 22 SER cc_start: 0.9218 (m) cc_final: 0.8978 (m) outliers start: 2 outliers final: 1 residues processed: 667 average time/residue: 0.2865 time to fit residues: 296.6789 Evaluate side-chains 516 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 514 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.0870 chunk 128 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 203 optimal weight: 0.0870 chunk 57 optimal weight: 9.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20371 Z= 0.189 Angle : 0.850 11.674 27674 Z= 0.398 Chirality : 0.054 0.460 3391 Planarity : 0.005 0.053 3389 Dihedral : 11.581 86.681 4566 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.52 % Favored : 88.39 % Rotamer: Outliers : 0.10 % Allowed : 3.07 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.69 (0.16), residues: 2343 helix: -1.51 (0.25), residues: 351 sheet: -1.50 (0.23), residues: 486 loop : -3.22 (0.14), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 596 HIS 0.005 0.001 HIS G 374 PHE 0.016 0.001 PHE I 320 TYR 0.046 0.002 TYR B 173 ARG 0.008 0.000 ARG H 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 665 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8441 (t0) cc_final: 0.7989 (t0) REVERT: A 620 SER cc_start: 0.8098 (p) cc_final: 0.7852 (p) REVERT: A 630 GLN cc_start: 0.8180 (mp10) cc_final: 0.7805 (mp10) REVERT: B 92 GLU cc_start: 0.4520 (pp20) cc_final: 0.4207 (pp20) REVERT: B 95 MET cc_start: 0.9038 (tmm) cc_final: 0.8647 (tmm) REVERT: B 96 TRP cc_start: 0.9394 (m100) cc_final: 0.8757 (m100) REVERT: B 98 ASN cc_start: 0.8185 (t0) cc_final: 0.7934 (t0) REVERT: B 106 GLU cc_start: 0.8080 (pt0) cc_final: 0.7832 (tm-30) REVERT: B 122 LEU cc_start: 0.7537 (tp) cc_final: 0.7316 (tt) REVERT: B 150 MET cc_start: 0.8713 (mmp) cc_final: 0.8103 (tpp) REVERT: B 171 LYS cc_start: 0.8354 (ptpp) cc_final: 0.8004 (ptpt) REVERT: B 195 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7208 (t160) REVERT: B 217 TYR cc_start: 0.4729 (m-10) cc_final: 0.4441 (m-10) REVERT: B 279 ASN cc_start: 0.6937 (t0) cc_final: 0.6484 (t0) REVERT: B 412 ASP cc_start: 0.7602 (m-30) cc_final: 0.7393 (t70) REVERT: B 474 ASP cc_start: 0.7604 (t70) cc_final: 0.6523 (t0) REVERT: B 492 GLU cc_start: 0.8203 (tp30) cc_final: 0.7722 (tt0) REVERT: C 530 MET cc_start: 0.9073 (ttm) cc_final: 0.8293 (mmm) REVERT: C 620 SER cc_start: 0.8394 (m) cc_final: 0.8148 (p) REVERT: C 658 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7732 (tp40) REVERT: D 22 CYS cc_start: 0.7935 (t) cc_final: 0.7403 (t) REVERT: D 47 GLU cc_start: 0.7703 (tp30) cc_final: 0.7428 (tp30) REVERT: D 52 ILE cc_start: 0.8186 (tp) cc_final: 0.7643 (tp) REVERT: D 57 ASN cc_start: 0.7487 (t0) cc_final: 0.7182 (t0) REVERT: D 61 ASN cc_start: 0.7478 (t0) cc_final: 0.7057 (t0) REVERT: D 67 ARG cc_start: 0.6571 (mmm160) cc_final: 0.5945 (mmm160) REVERT: D 70 ILE cc_start: 0.8540 (mp) cc_final: 0.8241 (mp) REVERT: E 31 PHE cc_start: 0.4068 (t80) cc_final: 0.3768 (t80) REVERT: E 92 ASP cc_start: 0.7977 (t0) cc_final: 0.7575 (m-30) REVERT: F 522 PHE cc_start: 0.7920 (t80) cc_final: 0.7567 (t80) REVERT: F 523 LEU cc_start: 0.8681 (mt) cc_final: 0.8441 (mt) REVERT: F 530 MET cc_start: 0.8956 (ttm) cc_final: 0.8392 (ttp) REVERT: F 543 ASN cc_start: 0.8261 (t0) cc_final: 0.7916 (t0) REVERT: F 630 GLN cc_start: 0.7902 (mp10) cc_final: 0.7632 (mp10) REVERT: F 638 TYR cc_start: 0.8146 (m-10) cc_final: 0.7872 (m-10) REVERT: F 664 ASP cc_start: 0.6881 (p0) cc_final: 0.6661 (p0) REVERT: G 82 GLN cc_start: 0.8547 (mm-40) cc_final: 0.7821 (mp10) REVERT: G 92 GLU cc_start: 0.6813 (pp20) cc_final: 0.6470 (pp20) REVERT: G 94 ASN cc_start: 0.7837 (t0) cc_final: 0.7453 (t0) REVERT: G 95 MET cc_start: 0.9336 (ptm) cc_final: 0.9108 (ptm) REVERT: G 98 ASN cc_start: 0.8872 (t0) cc_final: 0.8594 (t0) REVERT: G 164 GLU cc_start: 0.8902 (pp20) cc_final: 0.8448 (pp20) REVERT: G 195 ASN cc_start: 0.7254 (t0) cc_final: 0.6943 (t0) REVERT: G 289 ASN cc_start: 0.8015 (p0) cc_final: 0.7574 (p0) REVERT: G 321 ASP cc_start: 0.8369 (m-30) cc_final: 0.8166 (m-30) REVERT: G 325 ASP cc_start: 0.7608 (p0) cc_final: 0.7310 (p0) REVERT: G 363 GLN cc_start: 0.8208 (pp30) cc_final: 0.7895 (pp30) REVERT: G 453 ILE cc_start: 0.6795 (pt) cc_final: 0.6546 (pt) REVERT: G 477 ASP cc_start: 0.9194 (m-30) cc_final: 0.8876 (m-30) REVERT: G 492 GLU cc_start: 0.8331 (tp30) cc_final: 0.8073 (tp30) REVERT: G 499 THR cc_start: 0.6918 (t) cc_final: 0.6689 (t) REVERT: H 47 GLU cc_start: 0.7652 (tp30) cc_final: 0.7258 (tp30) REVERT: H 57 ASN cc_start: 0.6972 (t0) cc_final: 0.6767 (t0) REVERT: H 61 ASN cc_start: 0.6930 (t0) cc_final: 0.6641 (t0) REVERT: H 78 GLN cc_start: 0.7868 (mp10) cc_final: 0.6892 (mp10) REVERT: I 50 THR cc_start: 0.9065 (p) cc_final: 0.8710 (p) REVERT: I 53 PHE cc_start: 0.6661 (p90) cc_final: 0.6417 (p90) REVERT: I 71 THR cc_start: 0.8901 (m) cc_final: 0.8674 (m) REVERT: I 98 ASN cc_start: 0.8057 (t0) cc_final: 0.7653 (t0) REVERT: I 150 MET cc_start: 0.8161 (mpp) cc_final: 0.7360 (mpp) REVERT: I 173 TYR cc_start: 0.5035 (m-80) cc_final: 0.4686 (m-80) REVERT: I 195 ASN cc_start: 0.7399 (t0) cc_final: 0.7162 (t0) REVERT: I 211 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7519 (tm-30) REVERT: I 307 ILE cc_start: 0.7296 (mm) cc_final: 0.6987 (tp) REVERT: I 308 ARG cc_start: 0.7555 (mpp80) cc_final: 0.7278 (mtm-85) REVERT: I 321 ASP cc_start: 0.8841 (m-30) cc_final: 0.8616 (m-30) REVERT: I 328 MET cc_start: 0.7981 (ptm) cc_final: 0.7638 (ptp) REVERT: I 340 GLU cc_start: 0.8984 (tt0) cc_final: 0.8777 (tp30) REVERT: I 368 ASP cc_start: 0.6701 (t0) cc_final: 0.6147 (p0) REVERT: I 412 ASP cc_start: 0.7973 (m-30) cc_final: 0.7709 (t70) REVERT: I 479 TRP cc_start: 0.7842 (m-90) cc_final: 0.7492 (m-90) REVERT: J 40 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7879 (tm-30) REVERT: J 57 ASN cc_start: 0.6878 (t0) cc_final: 0.6546 (t0) REVERT: J 61 ASN cc_start: 0.6757 (t0) cc_final: 0.6373 (t0) REVERT: L 22 SER cc_start: 0.9173 (m) cc_final: 0.8627 (t) REVERT: L 31 PHE cc_start: 0.5050 (t80) cc_final: 0.4456 (t80) outliers start: 2 outliers final: 0 residues processed: 666 average time/residue: 0.2844 time to fit residues: 297.5701 Evaluate side-chains 523 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 522 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 118 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN G 99 ASN G 133 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20371 Z= 0.299 Angle : 0.893 11.245 27674 Z= 0.424 Chirality : 0.054 0.437 3391 Planarity : 0.005 0.053 3389 Dihedral : 11.407 83.021 4566 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.04 % Favored : 85.87 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.35 % 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: -3.66 (0.16), residues: 2343 helix: -1.39 (0.25), residues: 354 sheet: -1.29 (0.22), residues: 528 loop : -3.35 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 596 HIS 0.006 0.001 HIS I 374 PHE 0.022 0.002 PHE I 320 TYR 0.049 0.002 TYR B 173 ARG 0.010 0.001 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 642 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 LEU cc_start: 0.8810 (mt) cc_final: 0.8538 (mt) REVERT: A 543 ASN cc_start: 0.8372 (t0) cc_final: 0.7882 (t0) REVERT: A 570 HIS cc_start: 0.2739 (t70) cc_final: 0.2502 (t-90) REVERT: A 620 SER cc_start: 0.8100 (p) cc_final: 0.7805 (p) REVERT: A 630 GLN cc_start: 0.8259 (mp10) cc_final: 0.7805 (mp10) REVERT: B 96 TRP cc_start: 0.9246 (m100) cc_final: 0.8713 (m100) REVERT: B 98 ASN cc_start: 0.7941 (t0) cc_final: 0.7715 (t0) REVERT: B 106 GLU cc_start: 0.8209 (pt0) cc_final: 0.7925 (tm-30) REVERT: B 122 LEU cc_start: 0.7598 (tp) cc_final: 0.7381 (tt) REVERT: B 171 LYS cc_start: 0.8394 (ptpp) cc_final: 0.7890 (ptpt) REVERT: B 173 TYR cc_start: 0.5007 (m-80) cc_final: 0.3814 (m-80) REVERT: B 265 LEU cc_start: 0.7931 (mt) cc_final: 0.7380 (mm) REVERT: B 328 MET cc_start: 0.6535 (pmm) cc_final: 0.5875 (pmm) REVERT: B 474 ASP cc_start: 0.7838 (t70) cc_final: 0.6488 (t70) REVERT: B 475 MET cc_start: 0.6189 (mmm) cc_final: 0.5811 (mmm) REVERT: B 492 GLU cc_start: 0.8262 (tp30) cc_final: 0.8023 (tp30) REVERT: C 530 MET cc_start: 0.9171 (ttm) cc_final: 0.8560 (mmm) REVERT: C 620 SER cc_start: 0.8411 (m) cc_final: 0.8197 (p) REVERT: C 654 GLU cc_start: 0.8058 (pt0) cc_final: 0.7825 (pt0) REVERT: C 658 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7674 (tp40) REVERT: D 22 CYS cc_start: 0.7921 (t) cc_final: 0.7552 (t) REVERT: D 36 SER cc_start: 0.8713 (t) cc_final: 0.8482 (t) REVERT: D 40 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7512 (tm-30) REVERT: D 57 ASN cc_start: 0.7464 (t0) cc_final: 0.7150 (t0) REVERT: D 100 ASP cc_start: 0.9029 (t0) cc_final: 0.8653 (t0) REVERT: E 5 THR cc_start: 0.7595 (p) cc_final: 0.7193 (t) REVERT: E 60 ASP cc_start: 0.5650 (t0) cc_final: 0.5298 (t0) REVERT: E 85 ASP cc_start: 0.8672 (m-30) cc_final: 0.8388 (m-30) REVERT: F 522 PHE cc_start: 0.8057 (t80) cc_final: 0.7772 (t80) REVERT: F 523 LEU cc_start: 0.8815 (mt) cc_final: 0.8576 (mt) REVERT: F 528 SER cc_start: 0.7999 (m) cc_final: 0.7518 (p) REVERT: F 543 ASN cc_start: 0.8383 (t0) cc_final: 0.8081 (t0) REVERT: F 622 ILE cc_start: 0.8399 (mt) cc_final: 0.8132 (mt) REVERT: F 630 GLN cc_start: 0.7894 (mp10) cc_final: 0.7346 (mp10) REVERT: F 638 TYR cc_start: 0.8257 (m-10) cc_final: 0.8051 (m-10) REVERT: F 664 ASP cc_start: 0.7068 (p0) cc_final: 0.6838 (p0) REVERT: G 82 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7833 (mp10) REVERT: G 92 GLU cc_start: 0.7014 (pp20) cc_final: 0.6673 (pp20) REVERT: G 94 ASN cc_start: 0.8162 (t0) cc_final: 0.7787 (t0) REVERT: G 95 MET cc_start: 0.9234 (ptm) cc_final: 0.9010 (ptm) REVERT: G 98 ASN cc_start: 0.8726 (t0) cc_final: 0.8383 (t0) REVERT: G 106 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7908 (tm-30) REVERT: G 156 GLN cc_start: 0.7481 (pp30) cc_final: 0.7043 (pm20) REVERT: G 164 GLU cc_start: 0.8805 (pp20) cc_final: 0.8324 (pp20) REVERT: G 265 LEU cc_start: 0.8027 (mt) cc_final: 0.7750 (tp) REVERT: G 321 ASP cc_start: 0.8199 (m-30) cc_final: 0.7986 (m-30) REVERT: G 477 ASP cc_start: 0.9317 (m-30) cc_final: 0.9077 (m-30) REVERT: G 492 GLU cc_start: 0.8382 (tp30) cc_final: 0.8115 (tp30) REVERT: H 47 GLU cc_start: 0.7752 (tp30) cc_final: 0.7513 (tp30) REVERT: H 48 TRP cc_start: 0.8604 (t60) cc_final: 0.7898 (t60) REVERT: H 61 ASN cc_start: 0.7351 (t0) cc_final: 0.7059 (t0) REVERT: I 50 THR cc_start: 0.8946 (p) cc_final: 0.8681 (p) REVERT: I 71 THR cc_start: 0.8919 (m) cc_final: 0.8717 (m) REVERT: I 98 ASN cc_start: 0.8132 (t0) cc_final: 0.7829 (t0) REVERT: I 106 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7958 (tm-30) REVERT: I 195 ASN cc_start: 0.7671 (t0) cc_final: 0.7410 (t0) REVERT: I 205 CYS cc_start: 0.8050 (t) cc_final: 0.7718 (t) REVERT: I 289 ASN cc_start: 0.8017 (p0) cc_final: 0.7714 (p0) REVERT: I 308 ARG cc_start: 0.7551 (mpp80) cc_final: 0.7074 (mtm-85) REVERT: I 320 PHE cc_start: 0.7223 (t80) cc_final: 0.6492 (t80) REVERT: I 340 GLU cc_start: 0.9007 (tt0) cc_final: 0.8643 (tp30) REVERT: I 363 GLN cc_start: 0.8039 (pp30) cc_final: 0.7790 (pp30) REVERT: I 368 ASP cc_start: 0.6632 (t0) cc_final: 0.6213 (p0) REVERT: I 426 MET cc_start: 0.7922 (ptt) cc_final: 0.7411 (ptt) REVERT: J 40 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7590 (tm-30) REVERT: J 48 TRP cc_start: 0.8773 (t60) cc_final: 0.8250 (t60) REVERT: J 57 ASN cc_start: 0.7024 (t0) cc_final: 0.6679 (t0) REVERT: J 61 ASN cc_start: 0.7272 (t0) cc_final: 0.6764 (t0) REVERT: K 60 ASP cc_start: 0.6066 (t0) cc_final: 0.5579 (t0) REVERT: L 22 SER cc_start: 0.9162 (m) cc_final: 0.8638 (t) REVERT: L 60 ASP cc_start: 0.6019 (t0) cc_final: 0.5757 (t0) REVERT: L 85 ASP cc_start: 0.8415 (m-30) cc_final: 0.8122 (m-30) outliers start: 0 outliers final: 0 residues processed: 642 average time/residue: 0.2658 time to fit residues: 267.7928 Evaluate side-chains 496 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 651 ASN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN D 78 GLN F 540 GLN G 99 ASN G 103 GLN G 156 GLN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20371 Z= 0.260 Angle : 0.882 10.597 27674 Z= 0.418 Chirality : 0.054 0.440 3391 Planarity : 0.005 0.057 3389 Dihedral : 11.234 83.370 4566 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.06 % Favored : 86.90 % Rotamer: Outliers : 0.14 % Allowed : 2.73 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.31 % 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: -3.53 (0.16), residues: 2343 helix: -1.00 (0.27), residues: 336 sheet: -1.24 (0.24), residues: 486 loop : -3.27 (0.14), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 596 HIS 0.005 0.001 HIS G 374 PHE 0.019 0.002 PHE I 320 TYR 0.039 0.002 TYR B 173 ARG 0.005 0.001 ARG G 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 639 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 LEU cc_start: 0.8709 (mt) cc_final: 0.8440 (mt) REVERT: A 543 ASN cc_start: 0.8342 (t0) cc_final: 0.7895 (t0) REVERT: A 595 ILE cc_start: 0.8763 (tp) cc_final: 0.8550 (tp) REVERT: A 620 SER cc_start: 0.8121 (p) cc_final: 0.7829 (p) REVERT: A 651 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7162 (m-40) REVERT: B 49 GLU cc_start: 0.8434 (pp20) cc_final: 0.8115 (tm-30) REVERT: B 95 MET cc_start: 0.8962 (tmm) cc_final: 0.8742 (tmm) REVERT: B 96 TRP cc_start: 0.9147 (m100) cc_final: 0.8699 (m100) REVERT: B 106 GLU cc_start: 0.8185 (pt0) cc_final: 0.7965 (tm-30) REVERT: B 150 MET cc_start: 0.8708 (mmp) cc_final: 0.8503 (mpp) REVERT: B 265 LEU cc_start: 0.8077 (mt) cc_final: 0.7508 (mm) REVERT: B 368 ASP cc_start: 0.6607 (t70) cc_final: 0.6398 (t70) REVERT: B 474 ASP cc_start: 0.8003 (t70) cc_final: 0.6624 (t70) REVERT: C 530 MET cc_start: 0.9220 (ttm) cc_final: 0.8632 (mmm) REVERT: C 630 GLN cc_start: 0.8380 (mp10) cc_final: 0.8153 (mp10) REVERT: C 654 GLU cc_start: 0.8001 (pt0) cc_final: 0.7729 (pt0) REVERT: C 658 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7592 (tp40) REVERT: D 57 ASN cc_start: 0.7814 (t0) cc_final: 0.7448 (t0) REVERT: D 67 ARG cc_start: 0.7118 (mmm160) cc_final: 0.6718 (mmm160) REVERT: D 100 ASP cc_start: 0.9103 (t0) cc_final: 0.8843 (t0) REVERT: E 60 ASP cc_start: 0.5422 (t0) cc_final: 0.5031 (t0) REVERT: E 85 ASP cc_start: 0.8686 (m-30) cc_final: 0.8443 (m-30) REVERT: E 92 ASP cc_start: 0.8226 (t0) cc_final: 0.7907 (t0) REVERT: F 522 PHE cc_start: 0.8019 (t80) cc_final: 0.7780 (t80) REVERT: F 528 SER cc_start: 0.7799 (m) cc_final: 0.7414 (p) REVERT: F 543 ASN cc_start: 0.8512 (t0) cc_final: 0.8264 (t0) REVERT: F 576 LEU cc_start: 0.7593 (mp) cc_final: 0.7332 (tt) REVERT: F 622 ILE cc_start: 0.8443 (mt) cc_final: 0.8191 (mt) REVERT: F 630 GLN cc_start: 0.7984 (mp10) cc_final: 0.7338 (mp10) REVERT: F 638 TYR cc_start: 0.8241 (m-10) cc_final: 0.7994 (m-10) REVERT: F 664 ASP cc_start: 0.6688 (p0) cc_final: 0.6405 (p0) REVERT: G 52 LEU cc_start: 0.9112 (mt) cc_final: 0.8895 (mt) REVERT: G 82 GLN cc_start: 0.8566 (mm-40) cc_final: 0.7769 (mp10) REVERT: G 92 GLU cc_start: 0.6896 (pp20) cc_final: 0.6546 (pp20) REVERT: G 94 ASN cc_start: 0.7785 (t0) cc_final: 0.7362 (t0) REVERT: G 98 ASN cc_start: 0.8874 (t0) cc_final: 0.8637 (t0) REVERT: G 156 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7138 (pm20) REVERT: G 164 GLU cc_start: 0.8759 (pp20) cc_final: 0.8318 (pp20) REVERT: G 265 LEU cc_start: 0.8220 (mt) cc_final: 0.7972 (tp) REVERT: G 288 LEU cc_start: 0.7888 (mp) cc_final: 0.7618 (mp) REVERT: G 475 MET cc_start: 0.7315 (tpp) cc_final: 0.6846 (tpp) REVERT: G 492 GLU cc_start: 0.8364 (tp30) cc_final: 0.8085 (tp30) REVERT: H 40 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7285 (tp40) REVERT: H 48 TRP cc_start: 0.8576 (t60) cc_final: 0.7808 (t60) REVERT: H 61 ASN cc_start: 0.7512 (t0) cc_final: 0.7212 (t0) REVERT: H 67 ARG cc_start: 0.6707 (mmm160) cc_final: 0.6221 (mmm160) REVERT: I 32 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8872 (pm20) REVERT: I 50 THR cc_start: 0.9047 (p) cc_final: 0.8754 (p) REVERT: I 71 THR cc_start: 0.9040 (m) cc_final: 0.8776 (m) REVERT: I 98 ASN cc_start: 0.8211 (t0) cc_final: 0.7930 (t0) REVERT: I 106 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7965 (tm-30) REVERT: I 150 MET cc_start: 0.8289 (mpp) cc_final: 0.7447 (mpp) REVERT: I 195 ASN cc_start: 0.7805 (t0) cc_final: 0.7512 (t0) REVERT: I 289 ASN cc_start: 0.7842 (p0) cc_final: 0.7448 (p0) REVERT: I 308 ARG cc_start: 0.7484 (mpp80) cc_final: 0.7143 (mtm-85) REVERT: I 320 PHE cc_start: 0.7220 (t80) cc_final: 0.6698 (t80) REVERT: I 328 MET cc_start: 0.7609 (ptm) cc_final: 0.7382 (ptp) REVERT: I 340 GLU cc_start: 0.9068 (tt0) cc_final: 0.8743 (tp30) REVERT: I 363 GLN cc_start: 0.8126 (pp30) cc_final: 0.7757 (pp30) REVERT: I 368 ASP cc_start: 0.6672 (t0) cc_final: 0.6214 (p0) REVERT: I 426 MET cc_start: 0.8082 (ptt) cc_final: 0.7754 (ptt) REVERT: J 40 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7635 (tm-30) REVERT: J 48 TRP cc_start: 0.8857 (t60) cc_final: 0.8246 (t60) REVERT: J 57 ASN cc_start: 0.7223 (t0) cc_final: 0.6895 (t0) REVERT: J 61 ASN cc_start: 0.7451 (t0) cc_final: 0.6926 (t0) REVERT: J 100 ASP cc_start: 0.8914 (t0) cc_final: 0.8682 (t0) REVERT: K 31 PHE cc_start: 0.4848 (t80) cc_final: 0.4468 (t80) REVERT: K 60 ASP cc_start: 0.6106 (t0) cc_final: 0.5605 (t0) REVERT: L 22 SER cc_start: 0.9190 (m) cc_final: 0.8724 (t) REVERT: L 31 PHE cc_start: 0.5007 (t80) cc_final: 0.4542 (t80) REVERT: L 60 ASP cc_start: 0.6058 (t0) cc_final: 0.5780 (t0) REVERT: L 85 ASP cc_start: 0.8440 (m-30) cc_final: 0.8181 (m-30) outliers start: 3 outliers final: 0 residues processed: 640 average time/residue: 0.2816 time to fit residues: 284.5418 Evaluate side-chains 504 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 502 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 143 optimal weight: 0.0870 chunk 153 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN A 616 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN F 540 GLN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 170 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20371 Z= 0.252 Angle : 0.883 11.185 27674 Z= 0.417 Chirality : 0.054 0.522 3391 Planarity : 0.005 0.049 3389 Dihedral : 11.079 82.463 4566 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.44 % Favored : 86.51 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.26 % 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: -3.52 (0.16), residues: 2343 helix: -0.90 (0.28), residues: 333 sheet: -1.31 (0.23), residues: 525 loop : -3.29 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP J 100B HIS 0.005 0.001 HIS I 374 PHE 0.019 0.002 PHE I 320 TYR 0.034 0.002 TYR B 173 ARG 0.009 0.000 ARG A 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 628 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 LEU cc_start: 0.8718 (mt) cc_final: 0.8435 (mt) REVERT: A 543 ASN cc_start: 0.8380 (t0) cc_final: 0.7865 (t0) REVERT: A 620 SER cc_start: 0.8183 (p) cc_final: 0.7913 (p) REVERT: A 634 GLU cc_start: 0.9272 (mt-10) cc_final: 0.9029 (mt-10) REVERT: A 654 GLU cc_start: 0.8297 (pt0) cc_final: 0.8059 (pt0) REVERT: B 49 GLU cc_start: 0.8499 (pp20) cc_final: 0.8078 (tm-30) REVERT: B 96 TRP cc_start: 0.9157 (m100) cc_final: 0.8705 (m100) REVERT: B 104 MET cc_start: 0.7433 (ttp) cc_final: 0.6648 (ttp) REVERT: B 106 GLU cc_start: 0.8258 (pt0) cc_final: 0.7963 (tm-30) REVERT: B 150 MET cc_start: 0.8641 (mmp) cc_final: 0.8416 (mpp) REVERT: B 265 LEU cc_start: 0.8157 (mt) cc_final: 0.7594 (mm) REVERT: B 328 MET cc_start: 0.7299 (pmm) cc_final: 0.7015 (pmm) REVERT: B 499 THR cc_start: 0.7232 (t) cc_final: 0.7028 (t) REVERT: C 530 MET cc_start: 0.9243 (ttm) cc_final: 0.8657 (mmm) REVERT: C 538 THR cc_start: 0.7943 (p) cc_final: 0.7652 (p) REVERT: C 630 GLN cc_start: 0.8371 (mp10) cc_final: 0.8157 (mp10) REVERT: C 654 GLU cc_start: 0.7899 (pt0) cc_final: 0.7622 (pt0) REVERT: D 36 SER cc_start: 0.8624 (t) cc_final: 0.8404 (t) REVERT: D 57 ASN cc_start: 0.7749 (t0) cc_final: 0.7266 (t0) REVERT: E 49 TYR cc_start: 0.7348 (t80) cc_final: 0.6932 (t80) REVERT: E 60 ASP cc_start: 0.5455 (t0) cc_final: 0.5034 (t0) REVERT: E 85 ASP cc_start: 0.8551 (m-30) cc_final: 0.8280 (m-30) REVERT: E 92 ASP cc_start: 0.8204 (t0) cc_final: 0.7890 (t0) REVERT: F 528 SER cc_start: 0.7993 (m) cc_final: 0.7504 (p) REVERT: F 530 MET cc_start: 0.9212 (ttm) cc_final: 0.8771 (mmm) REVERT: F 543 ASN cc_start: 0.8366 (t0) cc_final: 0.8024 (t0) REVERT: F 622 ILE cc_start: 0.8412 (mt) cc_final: 0.8156 (mt) REVERT: F 638 TYR cc_start: 0.8242 (m-10) cc_final: 0.7975 (m-10) REVERT: F 664 ASP cc_start: 0.6562 (p0) cc_final: 0.6283 (p0) REVERT: G 82 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7596 (mp10) REVERT: G 92 GLU cc_start: 0.6758 (pp20) cc_final: 0.6412 (pp20) REVERT: G 94 ASN cc_start: 0.8058 (t0) cc_final: 0.7765 (t0) REVERT: G 138 LEU cc_start: 0.7898 (tt) cc_final: 0.7632 (tt) REVERT: G 156 GLN cc_start: 0.7496 (pp30) cc_final: 0.6972 (pm20) REVERT: G 164 GLU cc_start: 0.8655 (pp20) cc_final: 0.8395 (pp20) REVERT: G 265 LEU cc_start: 0.8345 (mt) cc_final: 0.8131 (tp) REVERT: G 475 MET cc_start: 0.7276 (tpp) cc_final: 0.6695 (tpp) REVERT: G 492 GLU cc_start: 0.8413 (tp30) cc_final: 0.8106 (tp30) REVERT: H 40 GLN cc_start: 0.7435 (tm-30) cc_final: 0.7134 (tm-30) REVERT: H 48 TRP cc_start: 0.8584 (t60) cc_final: 0.7858 (t60) REVERT: H 67 ARG cc_start: 0.6735 (mmm160) cc_final: 0.6174 (mmm160) REVERT: H 78 GLN cc_start: 0.7737 (mp10) cc_final: 0.7387 (mp10) REVERT: I 32 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8854 (pm20) REVERT: I 50 THR cc_start: 0.9039 (p) cc_final: 0.8769 (p) REVERT: I 71 THR cc_start: 0.9006 (m) cc_final: 0.8759 (m) REVERT: I 98 ASN cc_start: 0.8244 (t0) cc_final: 0.7968 (t0) REVERT: I 106 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7942 (tm-30) REVERT: I 150 MET cc_start: 0.8312 (mpp) cc_final: 0.7457 (mpp) REVERT: I 195 ASN cc_start: 0.7887 (t0) cc_final: 0.7588 (t0) REVERT: I 289 ASN cc_start: 0.7828 (p0) cc_final: 0.7468 (p0) REVERT: I 308 ARG cc_start: 0.7496 (mpp80) cc_final: 0.7120 (mtm-85) REVERT: I 328 MET cc_start: 0.7637 (ptm) cc_final: 0.7402 (ptp) REVERT: I 363 GLN cc_start: 0.8174 (pp30) cc_final: 0.7854 (pp30) REVERT: I 368 ASP cc_start: 0.6672 (t0) cc_final: 0.6230 (p0) REVERT: I 426 MET cc_start: 0.8024 (ptt) cc_final: 0.7497 (ptt) REVERT: J 40 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7638 (tm-30) REVERT: J 48 TRP cc_start: 0.8863 (t60) cc_final: 0.8203 (t60) REVERT: J 57 ASN cc_start: 0.7167 (t0) cc_final: 0.6914 (t0) REVERT: J 61 ASN cc_start: 0.7397 (t0) cc_final: 0.6967 (t0) REVERT: K 53 LYS cc_start: 0.6926 (mppt) cc_final: 0.6404 (mmtm) REVERT: K 54 ARG cc_start: 0.8576 (mmm-85) cc_final: 0.8049 (mmp80) REVERT: K 60 ASP cc_start: 0.5993 (t0) cc_final: 0.4280 (t0) REVERT: L 22 SER cc_start: 0.9142 (m) cc_final: 0.8799 (t) REVERT: L 31 PHE cc_start: 0.5189 (t80) cc_final: 0.4684 (t80) REVERT: L 60 ASP cc_start: 0.6054 (t0) cc_final: 0.5727 (t0) outliers start: 0 outliers final: 0 residues processed: 628 average time/residue: 0.2898 time to fit residues: 284.7505 Evaluate side-chains 513 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.8980 chunk 197 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN F 540 GLN F 616 ASN G 99 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 20371 Z= 0.268 Angle : 0.901 11.451 27674 Z= 0.426 Chirality : 0.055 0.747 3391 Planarity : 0.005 0.049 3389 Dihedral : 10.984 81.056 4566 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.62 % Favored : 86.34 % Rotamer: Outliers : 0.05 % Allowed : 0.81 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.18 % 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: -3.52 (0.16), residues: 2343 helix: -0.85 (0.28), residues: 333 sheet: -1.31 (0.23), residues: 525 loop : -3.31 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP J 100B HIS 0.004 0.001 HIS I 374 PHE 0.024 0.002 PHE C 522 TYR 0.027 0.002 TYR B 173 ARG 0.010 0.000 ARG A 617 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 618 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 LEU cc_start: 0.8718 (mt) cc_final: 0.8438 (mt) REVERT: A 530 MET cc_start: 0.8649 (tpp) cc_final: 0.8167 (tpp) REVERT: A 543 ASN cc_start: 0.8294 (t0) cc_final: 0.7836 (t0) REVERT: A 588 ARG cc_start: 0.8050 (ttt90) cc_final: 0.7635 (ttt180) REVERT: B 49 GLU cc_start: 0.8422 (pp20) cc_final: 0.8008 (tm-30) REVERT: B 96 TRP cc_start: 0.9210 (m100) cc_final: 0.8858 (m100) REVERT: B 100 MET cc_start: 0.7854 (ptp) cc_final: 0.7646 (ptp) REVERT: B 104 MET cc_start: 0.7702 (ttp) cc_final: 0.6962 (ttp) REVERT: B 106 GLU cc_start: 0.8252 (pt0) cc_final: 0.8042 (tm-30) REVERT: B 150 MET cc_start: 0.8626 (mmp) cc_final: 0.8396 (mpp) REVERT: B 205 CYS cc_start: 0.7849 (t) cc_final: 0.7645 (t) REVERT: B 265 LEU cc_start: 0.8016 (mt) cc_final: 0.7475 (mm) REVERT: B 328 MET cc_start: 0.7441 (pmm) cc_final: 0.7122 (pmm) REVERT: B 368 ASP cc_start: 0.6751 (t70) cc_final: 0.6502 (t70) REVERT: B 474 ASP cc_start: 0.8114 (t70) cc_final: 0.6964 (t0) REVERT: B 475 MET cc_start: 0.6934 (mmm) cc_final: 0.5867 (mmm) REVERT: B 479 TRP cc_start: 0.8429 (m-10) cc_final: 0.8093 (m-90) REVERT: B 492 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7274 (tt0) REVERT: C 530 MET cc_start: 0.9248 (ttm) cc_final: 0.8671 (mmm) REVERT: C 543 ASN cc_start: 0.8427 (t0) cc_final: 0.8146 (t0) REVERT: C 630 GLN cc_start: 0.8433 (mp10) cc_final: 0.8193 (mp10) REVERT: C 654 GLU cc_start: 0.7804 (pt0) cc_final: 0.7433 (pt0) REVERT: D 57 ASN cc_start: 0.8057 (t0) cc_final: 0.7691 (t0) REVERT: D 67 ARG cc_start: 0.7069 (mmm160) cc_final: 0.6738 (mmm160) REVERT: E 5 THR cc_start: 0.7722 (p) cc_final: 0.7455 (t) REVERT: E 49 TYR cc_start: 0.7305 (t80) cc_final: 0.6612 (t80) REVERT: E 60 ASP cc_start: 0.5602 (t0) cc_final: 0.5192 (t0) REVERT: E 85 ASP cc_start: 0.8569 (m-30) cc_final: 0.8269 (m-30) REVERT: E 92 ASP cc_start: 0.8211 (t0) cc_final: 0.7918 (t0) REVERT: F 528 SER cc_start: 0.7839 (m) cc_final: 0.7301 (p) REVERT: F 530 MET cc_start: 0.9148 (ttm) cc_final: 0.8743 (mmm) REVERT: F 543 ASN cc_start: 0.8384 (t0) cc_final: 0.8050 (t0) REVERT: F 588 ARG cc_start: 0.7890 (ttt180) cc_final: 0.7612 (tpt-90) REVERT: F 622 ILE cc_start: 0.8420 (mt) cc_final: 0.8161 (mt) REVERT: F 638 TYR cc_start: 0.8346 (m-10) cc_final: 0.8090 (m-10) REVERT: F 664 ASP cc_start: 0.6603 (p0) cc_final: 0.6319 (p0) REVERT: G 49 GLU cc_start: 0.7618 (tm-30) cc_final: 0.6633 (tm-30) REVERT: G 82 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7605 (mp10) REVERT: G 92 GLU cc_start: 0.6746 (pp20) cc_final: 0.6395 (pp20) REVERT: G 94 ASN cc_start: 0.7926 (t0) cc_final: 0.7554 (t0) REVERT: G 138 LEU cc_start: 0.8012 (tt) cc_final: 0.7770 (tt) REVERT: G 150 MET cc_start: 0.8902 (tpp) cc_final: 0.8584 (tpp) REVERT: G 164 GLU cc_start: 0.8609 (pp20) cc_final: 0.8306 (pp20) REVERT: G 492 GLU cc_start: 0.8406 (tp30) cc_final: 0.8101 (tp30) REVERT: H 40 GLN cc_start: 0.7451 (tm-30) cc_final: 0.7192 (tm-30) REVERT: H 48 TRP cc_start: 0.8616 (t60) cc_final: 0.7789 (t60) REVERT: H 67 ARG cc_start: 0.6734 (mmm160) cc_final: 0.6156 (mmm160) REVERT: I 32 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8935 (pm20) REVERT: I 71 THR cc_start: 0.9021 (m) cc_final: 0.8771 (m) REVERT: I 92 GLU cc_start: 0.8216 (pp20) cc_final: 0.7961 (pp20) REVERT: I 98 ASN cc_start: 0.8181 (t0) cc_final: 0.7917 (t0) REVERT: I 106 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7932 (tm-30) REVERT: I 150 MET cc_start: 0.8307 (mpp) cc_final: 0.7625 (mpp) REVERT: I 195 ASN cc_start: 0.7862 (t0) cc_final: 0.7557 (t0) REVERT: I 289 ASN cc_start: 0.7704 (p0) cc_final: 0.7329 (p0) REVERT: I 308 ARG cc_start: 0.7413 (mpp80) cc_final: 0.7087 (mtm-85) REVERT: I 340 GLU cc_start: 0.9005 (tt0) cc_final: 0.8612 (tp30) REVERT: I 368 ASP cc_start: 0.6659 (t0) cc_final: 0.6259 (p0) REVERT: I 479 TRP cc_start: 0.7371 (m-90) cc_final: 0.6238 (m-90) REVERT: J 40 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7638 (tm-30) REVERT: J 48 TRP cc_start: 0.8861 (t60) cc_final: 0.8214 (t60) REVERT: J 57 ASN cc_start: 0.7367 (t0) cc_final: 0.7148 (t0) REVERT: J 61 ASN cc_start: 0.7476 (t0) cc_final: 0.7069 (t0) REVERT: K 60 ASP cc_start: 0.6067 (t0) cc_final: 0.5474 (t0) REVERT: K 92 ASP cc_start: 0.8045 (t0) cc_final: 0.7825 (t70) REVERT: L 22 SER cc_start: 0.9128 (m) cc_final: 0.8806 (t) REVERT: L 31 PHE cc_start: 0.5211 (t80) cc_final: 0.4700 (t80) REVERT: L 53 LYS cc_start: 0.6777 (mppt) cc_final: 0.6562 (mptt) REVERT: L 60 ASP cc_start: 0.6194 (t0) cc_final: 0.5852 (t0) REVERT: L 85 ASP cc_start: 0.8630 (m-30) cc_final: 0.8380 (m-30) outliers start: 1 outliers final: 1 residues processed: 618 average time/residue: 0.2738 time to fit residues: 266.5861 Evaluate side-chains 501 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 500 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 214 optimal weight: 0.0050 chunk 185 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 78 GLN F 540 GLN G 99 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 ASN H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN K 38 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20371 Z= 0.218 Angle : 0.876 11.937 27674 Z= 0.411 Chirality : 0.054 0.568 3391 Planarity : 0.004 0.048 3389 Dihedral : 10.773 80.822 4566 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.93 % Favored : 87.03 % Rotamer: Outliers : 0.05 % Allowed : 0.53 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.45 (0.16), residues: 2343 helix: -0.99 (0.27), residues: 351 sheet: -1.28 (0.23), residues: 525 loop : -3.21 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP J 100B HIS 0.004 0.001 HIS I 374 PHE 0.024 0.001 PHE C 522 TYR 0.032 0.002 TYR B 173 ARG 0.007 0.000 ARG A 617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 631 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 LEU cc_start: 0.8683 (mt) cc_final: 0.8404 (mt) REVERT: A 530 MET cc_start: 0.8714 (tpp) cc_final: 0.8325 (tpp) REVERT: A 543 ASN cc_start: 0.8241 (t0) cc_final: 0.7853 (t0) REVERT: A 588 ARG cc_start: 0.8027 (ttt90) cc_final: 0.7632 (ttt180) REVERT: A 654 GLU cc_start: 0.8363 (pt0) cc_final: 0.8138 (pt0) REVERT: B 49 GLU cc_start: 0.8337 (pp20) cc_final: 0.8084 (tm-30) REVERT: B 95 MET cc_start: 0.8894 (tmm) cc_final: 0.8563 (tmm) REVERT: B 96 TRP cc_start: 0.9193 (m100) cc_final: 0.8750 (m100) REVERT: B 98 ASN cc_start: 0.8198 (t0) cc_final: 0.7961 (t0) REVERT: B 104 MET cc_start: 0.7545 (ttp) cc_final: 0.6786 (ttp) REVERT: B 205 CYS cc_start: 0.7946 (t) cc_final: 0.7744 (t) REVERT: B 265 LEU cc_start: 0.7957 (mt) cc_final: 0.7462 (mm) REVERT: B 300 ASN cc_start: 0.8272 (m110) cc_final: 0.8031 (m110) REVERT: B 321 ASP cc_start: 0.8461 (m-30) cc_final: 0.8246 (m-30) REVERT: B 328 MET cc_start: 0.7400 (pmm) cc_final: 0.7099 (pmm) REVERT: B 368 ASP cc_start: 0.6727 (t70) cc_final: 0.6516 (t70) REVERT: B 384 TYR cc_start: 0.6973 (m-80) cc_final: 0.6673 (m-80) REVERT: B 474 ASP cc_start: 0.8053 (t70) cc_final: 0.6890 (t0) REVERT: B 475 MET cc_start: 0.6892 (mmm) cc_final: 0.5790 (mmm) REVERT: B 479 TRP cc_start: 0.8348 (m-10) cc_final: 0.8028 (m-90) REVERT: B 492 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7266 (tt0) REVERT: B 499 THR cc_start: 0.7425 (t) cc_final: 0.7211 (t) REVERT: C 530 MET cc_start: 0.9260 (ttm) cc_final: 0.8671 (mmm) REVERT: C 543 ASN cc_start: 0.8395 (t0) cc_final: 0.8180 (t0) REVERT: C 630 GLN cc_start: 0.8386 (mp10) cc_final: 0.8174 (mp10) REVERT: C 654 GLU cc_start: 0.7820 (pt0) cc_final: 0.7462 (pt0) REVERT: D 36 SER cc_start: 0.8662 (t) cc_final: 0.8460 (t) REVERT: D 57 ASN cc_start: 0.8043 (t0) cc_final: 0.7660 (t0) REVERT: D 67 ARG cc_start: 0.7014 (mmm160) cc_final: 0.6667 (mmm160) REVERT: E 49 TYR cc_start: 0.7224 (t80) cc_final: 0.6568 (t80) REVERT: E 60 ASP cc_start: 0.5699 (t0) cc_final: 0.5268 (t0) REVERT: E 85 ASP cc_start: 0.8564 (m-30) cc_final: 0.8249 (m-30) REVERT: E 92 ASP cc_start: 0.8065 (t0) cc_final: 0.7770 (t0) REVERT: F 522 PHE cc_start: 0.7886 (t80) cc_final: 0.7614 (t80) REVERT: F 528 SER cc_start: 0.7816 (m) cc_final: 0.7279 (p) REVERT: F 530 MET cc_start: 0.9217 (ttm) cc_final: 0.8870 (mmm) REVERT: F 543 ASN cc_start: 0.8381 (t0) cc_final: 0.8055 (t0) REVERT: F 588 ARG cc_start: 0.7889 (ttt180) cc_final: 0.7602 (tpt-90) REVERT: F 622 ILE cc_start: 0.8332 (mt) cc_final: 0.8073 (mt) REVERT: F 638 TYR cc_start: 0.8515 (m-10) cc_final: 0.8182 (m-10) REVERT: F 664 ASP cc_start: 0.5953 (p0) cc_final: 0.5734 (p0) REVERT: G 49 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6492 (tm-30) REVERT: G 83 GLU cc_start: 0.8718 (pp20) cc_final: 0.8249 (tm-30) REVERT: G 84 ILE cc_start: 0.8148 (mm) cc_final: 0.7832 (mm) REVERT: G 92 GLU cc_start: 0.6765 (pp20) cc_final: 0.6417 (pp20) REVERT: G 94 ASN cc_start: 0.7588 (t0) cc_final: 0.7193 (t0) REVERT: G 98 ASN cc_start: 0.8665 (t0) cc_final: 0.8372 (t0) REVERT: G 138 LEU cc_start: 0.8031 (tt) cc_final: 0.7644 (tt) REVERT: G 164 GLU cc_start: 0.8588 (pp20) cc_final: 0.8327 (pp20) REVERT: G 328 MET cc_start: 0.7411 (pmm) cc_final: 0.6736 (pmm) REVERT: G 492 GLU cc_start: 0.8384 (tp30) cc_final: 0.7785 (tt0) REVERT: H 48 TRP cc_start: 0.8669 (t60) cc_final: 0.7953 (t60) REVERT: H 67 ARG cc_start: 0.6773 (mmm160) cc_final: 0.6545 (mmm160) REVERT: I 32 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8956 (pm20) REVERT: I 71 THR cc_start: 0.8968 (m) cc_final: 0.8715 (m) REVERT: I 82 GLN cc_start: 0.8512 (mm-40) cc_final: 0.7655 (mp10) REVERT: I 92 GLU cc_start: 0.8216 (pp20) cc_final: 0.7953 (pp20) REVERT: I 98 ASN cc_start: 0.8136 (t0) cc_final: 0.7872 (t0) REVERT: I 106 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7923 (tm-30) REVERT: I 150 MET cc_start: 0.8236 (mpp) cc_final: 0.7767 (mpp) REVERT: I 195 ASN cc_start: 0.7798 (t0) cc_final: 0.7451 (t0) REVERT: I 205 CYS cc_start: 0.8462 (t) cc_final: 0.8242 (t) REVERT: I 289 ASN cc_start: 0.7622 (p0) cc_final: 0.7262 (p0) REVERT: I 308 ARG cc_start: 0.7561 (mpp80) cc_final: 0.7211 (mtm-85) REVERT: I 328 MET cc_start: 0.7676 (ptm) cc_final: 0.7294 (ptp) REVERT: I 340 GLU cc_start: 0.8994 (tt0) cc_final: 0.8603 (tp30) REVERT: I 363 GLN cc_start: 0.8230 (pp30) cc_final: 0.7878 (pp30) REVERT: I 368 ASP cc_start: 0.6620 (t0) cc_final: 0.6269 (p0) REVERT: I 426 MET cc_start: 0.8076 (ptt) cc_final: 0.7571 (ptt) REVERT: I 479 TRP cc_start: 0.7348 (m-90) cc_final: 0.6269 (m-90) REVERT: J 40 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7637 (tm-30) REVERT: J 48 TRP cc_start: 0.8860 (t60) cc_final: 0.8264 (t60) REVERT: J 57 ASN cc_start: 0.7537 (t0) cc_final: 0.7328 (t0) REVERT: J 61 ASN cc_start: 0.7416 (t0) cc_final: 0.7052 (t0) REVERT: K 60 ASP cc_start: 0.6149 (t0) cc_final: 0.5540 (t0) REVERT: L 22 SER cc_start: 0.9105 (m) cc_final: 0.8801 (t) REVERT: L 31 PHE cc_start: 0.5297 (t80) cc_final: 0.4769 (t80) REVERT: L 60 ASP cc_start: 0.6257 (t0) cc_final: 0.5898 (t0) REVERT: L 92 ASP cc_start: 0.8011 (t70) cc_final: 0.7564 (t70) outliers start: 1 outliers final: 0 residues processed: 632 average time/residue: 0.2776 time to fit residues: 277.3828 Evaluate side-chains 516 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 0.2980 chunk 77 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN D 78 GLN E 38 GLN F 540 GLN G 99 ASN G 103 GLN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 ASN G 203 GLN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.119792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094958 restraints weight = 41867.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.097886 restraints weight = 25637.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099949 restraints weight = 18202.323| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20371 Z= 0.328 Angle : 0.943 12.677 27674 Z= 0.447 Chirality : 0.055 0.558 3391 Planarity : 0.005 0.058 3389 Dihedral : 10.986 77.410 4566 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 15.45 % Favored : 84.51 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.51 (0.16), residues: 2343 helix: -0.82 (0.28), residues: 321 sheet: -1.46 (0.21), residues: 591 loop : -3.27 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP E 35 HIS 0.005 0.001 HIS I 374 PHE 0.027 0.002 PHE C 522 TYR 0.050 0.002 TYR B 173 ARG 0.008 0.001 ARG A 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5353.84 seconds wall clock time: 95 minutes 37.49 seconds (5737.49 seconds total)