Starting phenix.real_space_refine on Fri Apr 12 05:22:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uot_26653/04_2024/7uot_26653.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uot_26653/04_2024/7uot_26653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uot_26653/04_2024/7uot_26653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uot_26653/04_2024/7uot_26653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uot_26653/04_2024/7uot_26653.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uot_26653/04_2024/7uot_26653.pdb" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7980 atoms to isotropic. 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 112 5.16 5 C 10505 2.51 5 N 2677 2.21 5 O 3540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "T TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16834 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1521 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "a" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1224 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "T" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "S" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1521 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "b" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1224 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "P" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "O" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "C" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1521 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "c" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1224 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "R" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "Q" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "H" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1048 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "L" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 794 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "I" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "V" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "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: 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "g" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "k" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "l" 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: "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: 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: "q" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "u" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 9.32, per 1000 atoms: 0.55 Number of scatterers: 16834 At special positions: 0 Unit cell: (138.6, 147.84, 124.74, 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 112 16.00 O 3540 8.00 N 2677 7.00 C 10505 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN g 4 " - " MAN g 5 " " MAN r 4 " - " MAN r 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA M 3 " - " MAN M 4 " " BMA V 3 " - " MAN V 4 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " BMA u 3 " - " MAN u 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA M 3 " - " MAN M 6 " " BMA V 3 " - " MAN V 5 " " BMA Z 3 " - " MAN Z 4 " " BMA g 3 " - " MAN g 6 " " BMA j 3 " - " MAN j 5 " " BMA q 3 " - " MAN q 5 " " BMA r 3 " - " MAN r 6 " " BMA u 3 " - " MAN u 5 " BETA1-3 " NAG f 1 " - " FUC f 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 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 M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 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 X 2 " - " BMA X 3 " " 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 d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " 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 q 2 " - " BMA q 3 " " 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 u 2 " - " BMA u 3 " BETA1-6 " NAG G 1 " - " FUC G 4 " " NAG I 1 " - " FUC I 6 " " NAG U 1 " - " FUC U 3 " " NAG V 1 " - " FUC V 6 " " NAG X 1 " - " FUC X 4 " " NAG i 1 " - " FUC i 3 " " NAG j 1 " - " FUC j 6 " " NAG k 1 " - " FUC k 4 " " NAG q 1 " - " FUC q 6 " " NAG t 1 " - " FUC t 3 " " NAG u 1 " - " FUC u 6 " NAG-ASN " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 99 " " NAG G 1 " - " ASN A 109 " " NAG I 1 " - " ASN A 119 " " NAG J 1 " - " ASN A 167 " " NAG K 1 " - " ASN A 224 " " NAG M 1 " - " ASN a 365 " " NAG N 1 " - " ASN a 373 " " NAG U 1 " - " ASN a 390 " " NAG V 1 " - " ASN a 395 " " NAG W 1 " - " ASN B 89 " " NAG X 1 " - " ASN B 109 " " NAG Y 1 " - " ASN B 167 " " NAG Z 1 " - " ASN B 79 " " NAG d 1 " - " ASN B 99 " " NAG e 1 " - " ASN B 224 " " NAG f 1 " - " ASN B 119 " " NAG g 1 " - " ASN b 365 " " NAG h 1 " - " ASN b 373 " " NAG i 1 " - " ASN b 390 " " NAG j 1 " - " ASN b 395 " " NAG k 1 " - " ASN C 109 " " NAG l 1 " - " ASN C 79 " " NAG m 1 " - " ASN C 89 " " NAG n 1 " - " ASN C 99 " " NAG o 1 " - " ASN C 167 " " NAG p 1 " - " ASN C 224 " " NAG q 1 " - " ASN C 119 " " NAG r 1 " - " ASN c 365 " " NAG s 1 " - " ASN c 373 " " NAG t 1 " - " ASN c 390 " " NAG u 1 " - " ASN c 395 " Time building additional restraints: 8.06 Conformation dependent library (CDL) restraints added in 2.6 seconds 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3610 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 35 sheets defined 24.3% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.806A pdb=" N GLY A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 198 through 203 removed outlier: 4.102A pdb=" N ILE A 201 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'a' and resid 294 through 300 removed outlier: 3.911A pdb=" N LYS a 300 " --> pdb=" O THR a 296 " (cutoff:3.500A) Processing helix chain 'a' and resid 301 through 303 No H-bonds generated for 'chain 'a' and resid 301 through 303' Processing helix chain 'a' and resid 307 through 326 removed outlier: 3.608A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 334 through 341 Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.875A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 416 Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.760A pdb=" N PHE T 83 " --> pdb=" O SER T 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.936A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.718A pdb=" N LYS B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.636A pdb=" N ILE B 201 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP B 204 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 4.214A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 300 removed outlier: 3.808A pdb=" N LYS b 300 " --> pdb=" O THR b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 301 through 303 No H-bonds generated for 'chain 'b' and resid 301 through 303' Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 334 through 340 Processing helix chain 'b' and resid 346 through 360 removed outlier: 3.843A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 416 removed outlier: 3.563A pdb=" N GLN b 416 " --> pdb=" O THR b 412 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.662A pdb=" N TYR O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.704A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.839A pdb=" N ASP C 204 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 334 through 341 Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.899A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 416 removed outlier: 3.660A pdb=" N GLN c 416 " --> pdb=" O THR c 412 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.509A pdb=" N TYR Q 32 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 65 removed outlier: 4.005A pdb=" N GLN Q 65 " --> pdb=" O GLN Q 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 62 through 65' Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.928A pdb=" N THR Q 91 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.578A pdb=" N GLY H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.586A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'L' and resid 26 through 29 Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.507A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 156 removed outlier: 5.650A pdb=" N THR A 87 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG A 235 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AA4, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'T' and resid 4 through 5 removed outlier: 12.301A pdb=" N CYS T 23 " --> pdb=" O THR T 74 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N THR T 74 " --> pdb=" O CYS T 23 " (cutoff:3.500A) removed outlier: 11.951A pdb=" N ALA T 25 " --> pdb=" O THR T 72 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N THR T 72 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 11.249A pdb=" N GLN T 27 " --> pdb=" O GLU T 70 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLU T 70 " --> pdb=" O GLN T 27 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY T 68 " --> pdb=" O VAL T 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 53 through 54 removed outlier: 6.438A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER T 97 " --> pdb=" O GLN T 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'T' and resid 53 through 54 removed outlier: 6.438A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 4 through 5 removed outlier: 3.534A pdb=" N VAL S 5 " --> pdb=" O LYS S 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 11 removed outlier: 3.524A pdb=" N THR S 125 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE S 34 " --> pdb=" O TRP S 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TRP S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 11 removed outlier: 3.524A pdb=" N THR S 125 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL S 117 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AB3, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.563A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB5, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AB6, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.615A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 10 through 11 removed outlier: 3.821A pdb=" N SER P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AC1, first strand: chain 'O' and resid 10 through 11 removed outlier: 3.858A pdb=" N THR O 125 " --> pdb=" O GLU O 10 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AC3, first strand: chain 'C' and resid 83 through 87 removed outlier: 3.660A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AC5, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AC6, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AC7, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.504A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER R 97 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.504A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.578A pdb=" N GLU Q 10 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR Q 125 " --> pdb=" O GLU Q 10 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 10 through 11 removed outlier: 3.578A pdb=" N GLU Q 10 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR Q 125 " --> pdb=" O GLU Q 10 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL Q 117 " --> pdb=" O ARG Q 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.696A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP H 35 " --> pdb=" O ASN H 51 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 127 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.696A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP H 35 " --> pdb=" O ASN H 51 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AD7, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.475A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.475A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1626 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: 6.10 Time building geometry restraints manager: 8.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5058 1.34 - 1.46: 4126 1.46 - 1.58: 7821 1.58 - 1.70: 1 1.70 - 1.82: 172 Bond restraints: 17178 Sorted by residual: bond pdb=" C1 NAG q 1 " pdb=" O5 NAG q 1 " ideal model delta sigma weight residual 1.406 1.338 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1 BMA j 3 " pdb=" C2 BMA j 3 " ideal model delta sigma weight residual 1.519 1.580 -0.061 2.00e-02 2.50e+03 9.37e+00 bond pdb=" C5 BMA q 3 " pdb=" O5 BMA q 3 " ideal model delta sigma weight residual 1.417 1.471 -0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" N LEU a 387 " pdb=" CA LEU a 387 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.27e-02 6.20e+03 7.04e+00 bond pdb=" C1 BMA j 3 " pdb=" O5 BMA j 3 " ideal model delta sigma weight residual 1.410 1.463 -0.053 2.00e-02 2.50e+03 6.91e+00 ... (remaining 17173 not shown) Histogram of bond angle deviations from ideal: 97.61 - 104.95: 220 104.95 - 112.30: 9367 112.30 - 119.64: 5589 119.64 - 126.99: 7936 126.99 - 134.33: 199 Bond angle restraints: 23311 Sorted by residual: angle pdb=" C GLN C 223 " pdb=" N ASN C 224 " pdb=" CA ASN C 224 " ideal model delta sigma weight residual 122.67 112.91 9.76 1.73e+00 3.34e-01 3.19e+01 angle pdb=" N ASN C 224 " pdb=" CA ASN C 224 " pdb=" CB ASN C 224 " ideal model delta sigma weight residual 110.46 117.36 -6.90 1.55e+00 4.16e-01 1.98e+01 angle pdb=" CA PHE a 399 " pdb=" CB PHE a 399 " pdb=" CG PHE a 399 " ideal model delta sigma weight residual 113.80 117.96 -4.16 1.00e+00 1.00e+00 1.73e+01 angle pdb=" N ASN C 109 " pdb=" CA ASN C 109 " pdb=" C ASN C 109 " ideal model delta sigma weight residual 113.19 107.16 6.03 1.58e+00 4.01e-01 1.45e+01 angle pdb=" C ASN C 109 " pdb=" CA ASN C 109 " pdb=" CB ASN C 109 " ideal model delta sigma weight residual 110.35 116.71 -6.36 1.78e+00 3.16e-01 1.28e+01 ... (remaining 23306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.30: 10681 25.30 - 50.59: 597 50.59 - 75.89: 131 75.89 - 101.18: 133 101.18 - 126.48: 66 Dihedral angle restraints: 11608 sinusoidal: 5954 harmonic: 5654 Sorted by residual: dihedral pdb=" CB CYS c 364 " pdb=" SG CYS c 364 " pdb=" SG CYS c 385 " pdb=" CB CYS c 385 " ideal model delta sinusoidal sigma weight residual -86.00 -169.06 83.06 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" CB CYS b 364 " pdb=" SG CYS b 364 " pdb=" SG CYS b 385 " pdb=" CB CYS b 385 " ideal model delta sinusoidal sigma weight residual -86.00 -165.52 79.52 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " pdb=" SG CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sinusoidal sigma weight residual -86.00 -164.62 78.62 1 1.00e+01 1.00e-02 7.71e+01 ... (remaining 11605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.244: 2903 0.244 - 0.489: 21 0.489 - 0.733: 0 0.733 - 0.978: 2 0.978 - 1.222: 1 Chirality restraints: 2927 Sorted by residual: chirality pdb=" C1 FUC V 6 " pdb=" O6 NAG V 1 " pdb=" C2 FUC V 6 " pdb=" O5 FUC V 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.39e+02 chirality pdb=" C1 MAN M 5 " pdb=" O2 MAN M 4 " pdb=" C2 MAN M 5 " pdb=" O5 MAN M 5 " both_signs ideal model delta sigma weight residual False 2.40 2.21 0.19 2.00e-02 2.50e+03 8.94e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.41e+01 ... (remaining 2924 not shown) Planarity restraints: 2807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " -0.155 2.00e-02 2.50e+03 1.28e-01 2.04e+02 pdb=" C7 NAG V 1 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " -0.115 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " 0.205 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 2 " 0.139 2.00e-02 2.50e+03 1.15e-01 1.65e+02 pdb=" C7 NAG V 2 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG V 2 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG V 2 " -0.185 2.00e-02 2.50e+03 pdb=" O7 NAG V 2 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 109 " 0.055 2.00e-02 2.50e+03 4.93e-02 3.04e+01 pdb=" CG ASN C 109 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN C 109 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 109 " -0.050 2.00e-02 2.50e+03 pdb=" C1 NAG k 1 " 0.054 2.00e-02 2.50e+03 ... (remaining 2804 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1491 2.74 - 3.28: 16046 3.28 - 3.82: 26818 3.82 - 4.36: 33264 4.36 - 4.90: 57397 Nonbonded interactions: 135016 Sorted by model distance: nonbonded pdb=" OH TYR R 36 " pdb=" OE1 GLN R 89 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASN C 99 " pdb=" N2 NAG n 1 " model vdw 2.253 2.520 nonbonded pdb=" NH2 ARG a 356 " pdb=" O GLY O 108 " model vdw 2.255 2.520 nonbonded pdb=" NH2 ARG b 356 " pdb=" O GLY Q 108 " model vdw 2.258 2.520 nonbonded pdb=" O3 NAG J 2 " pdb=" O2 BMA J 3 " model vdw 2.274 2.440 ... (remaining 135011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'l' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'p' and resid 1) selection = (chain 't' and resid 1) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'K' selection = chain 'N' selection = chain 'W' selection = chain 'd' selection = chain 'e' selection = chain 'h' selection = chain 'm' selection = chain 'n' selection = chain 's' } ncs_group { reference = (chain 'G' and resid 1 through 3) selection = (chain 'X' and resid 1 through 3) selection = (chain 'Z' and resid 1 through 3) selection = (chain 'k' and resid 1 through 3) } ncs_group { reference = (chain 'I' and resid 1 through 5) selection = (chain 'M' and resid 1 through 5) selection = (chain 'V' and resid 1 through 5) selection = (chain 'g' and resid 1 through 5) selection = (chain 'j' and resid 1 through 5) selection = (chain 'q' and resid 1 through 5) selection = (chain 'r' and resid 1 through 5) selection = (chain 'u' and resid 1 through 5) } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 28.070 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 47.260 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.006 0.068 17178 Z= 0.406 Angle : 0.863 9.765 23311 Z= 0.390 Chirality : 0.063 1.222 2927 Planarity : 0.005 0.128 2774 Dihedral : 20.946 126.481 7920 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.20), residues: 1916 helix: 1.05 (0.29), residues: 350 sheet: 0.73 (0.24), residues: 506 loop : -0.20 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 386 HIS 0.006 0.001 HIS B 230 PHE 0.021 0.001 PHE a 399 TYR 0.014 0.001 TYR T 91 ARG 0.010 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 120 GLN cc_start: 0.8364 (pp30) cc_final: 0.7704 (pp30) REVERT: R 24 ARG cc_start: 0.7622 (ttm110) cc_final: 0.7233 (ttm110) REVERT: R 61 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7870 (ttp-110) REVERT: Q 38 ARG cc_start: 0.8464 (ttp-170) cc_final: 0.7508 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 341 average time/residue: 1.6532 time to fit residues: 613.8369 Evaluate side-chains 309 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 307 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain Q residue 73 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 348 GLN B 185 ASN B 189 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 295 ASN ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN c 405 GLN R 100 GLN L 62 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17178 Z= 0.376 Angle : 0.744 10.626 23311 Z= 0.346 Chirality : 0.051 0.788 2927 Planarity : 0.004 0.043 2774 Dihedral : 17.291 113.561 4441 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.77 % Allowed : 11.47 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1916 helix: 1.12 (0.29), residues: 350 sheet: 0.79 (0.24), residues: 504 loop : -0.29 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 386 HIS 0.004 0.001 HIS a 305 PHE 0.018 0.001 PHE b 399 TYR 0.017 0.002 TYR T 91 ARG 0.007 0.001 ARG a 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 318 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7244 (ttp80) REVERT: S 120 GLN cc_start: 0.8471 (pp30) cc_final: 0.7878 (pp30) REVERT: R 24 ARG cc_start: 0.7640 (ttm110) cc_final: 0.7269 (ttm110) REVERT: R 61 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7870 (ttp-110) outliers start: 30 outliers final: 8 residues processed: 322 average time/residue: 1.6331 time to fit residues: 573.2989 Evaluate side-chains 320 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 311 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain a residue 396 GLU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 100 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 144 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN B 185 ASN B 189 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 295 ASN ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17178 Z= 0.183 Angle : 0.655 11.324 23311 Z= 0.300 Chirality : 0.047 0.684 2927 Planarity : 0.003 0.042 2774 Dihedral : 14.326 103.759 4437 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.77 % Allowed : 14.84 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1916 helix: 1.41 (0.29), residues: 353 sheet: 0.72 (0.24), residues: 524 loop : -0.20 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 210 HIS 0.002 0.001 HIS A 141 PHE 0.012 0.001 PHE b 399 TYR 0.012 0.001 TYR R 49 ARG 0.007 0.001 ARG a 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 322 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7243 (ttp80) REVERT: T 103 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7745 (ttp80) REVERT: S 12 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8043 (ptmm) REVERT: S 120 GLN cc_start: 0.8402 (pp30) cc_final: 0.7969 (pp30) REVERT: B 75 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7534 (mmt) REVERT: R 24 ARG cc_start: 0.7581 (ttm110) cc_final: 0.7258 (ttm110) outliers start: 30 outliers final: 10 residues processed: 332 average time/residue: 1.5718 time to fit residues: 572.3225 Evaluate side-chains 321 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 308 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN B 189 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 295 ASN ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17178 Z= 0.365 Angle : 0.727 13.238 23311 Z= 0.336 Chirality : 0.050 0.778 2927 Planarity : 0.004 0.044 2774 Dihedral : 13.009 103.369 4437 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.78 % Allowed : 16.97 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1916 helix: 1.33 (0.29), residues: 350 sheet: 0.60 (0.23), residues: 530 loop : -0.22 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 109 HIS 0.004 0.001 HIS a 305 PHE 0.017 0.002 PHE a 399 TYR 0.017 0.001 TYR T 91 ARG 0.007 0.001 ARG a 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 307 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7265 (ttp80) REVERT: T 103 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7770 (ttp80) REVERT: S 12 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8171 (ptmm) REVERT: S 120 GLN cc_start: 0.8370 (pp30) cc_final: 0.7885 (pp30) REVERT: C 183 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8242 (m) REVERT: R 24 ARG cc_start: 0.7665 (ttm110) cc_final: 0.7262 (ttm110) REVERT: Q 38 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.7471 (ttm170) outliers start: 47 outliers final: 16 residues processed: 329 average time/residue: 1.5584 time to fit residues: 561.2510 Evaluate side-chains 323 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 303 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain a residue 396 GLU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain Q residue 38 ARG Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN B 189 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 295 ASN ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN R 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17178 Z= 0.198 Angle : 0.658 10.163 23311 Z= 0.302 Chirality : 0.046 0.706 2927 Planarity : 0.004 0.042 2774 Dihedral : 11.941 100.834 4437 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.42 % Allowed : 18.10 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1916 helix: 1.44 (0.29), residues: 353 sheet: 0.67 (0.23), residues: 524 loop : -0.18 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 35 HIS 0.003 0.001 HIS A 141 PHE 0.012 0.001 PHE b 399 TYR 0.012 0.001 TYR L 51 ARG 0.013 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 310 time to evaluate : 1.892 Fit side-chains revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7246 (ttp80) REVERT: T 103 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7754 (ttp80) REVERT: S 12 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8096 (ptmm) REVERT: S 120 GLN cc_start: 0.8344 (pp30) cc_final: 0.7655 (pp30) REVERT: B 247 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8457 (tm-30) REVERT: O 38 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8575 (ttm170) REVERT: R 24 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7255 (ttm110) REVERT: L 56 ARG cc_start: 0.8758 (mtm-85) cc_final: 0.8544 (mtm110) outliers start: 41 outliers final: 16 residues processed: 329 average time/residue: 1.5731 time to fit residues: 565.9596 Evaluate side-chains 323 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 303 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 153 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN T 100 GLN B 185 ASN B 189 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 295 ASN ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17178 Z= 0.230 Angle : 0.664 10.459 23311 Z= 0.306 Chirality : 0.046 0.706 2927 Planarity : 0.004 0.042 2774 Dihedral : 11.270 100.528 4437 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.72 % Allowed : 18.69 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1916 helix: 1.48 (0.29), residues: 353 sheet: 0.68 (0.23), residues: 524 loop : -0.19 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 210 HIS 0.003 0.001 HIS a 305 PHE 0.016 0.001 PHE R 98 TYR 0.013 0.001 TYR T 91 ARG 0.012 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 310 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7269 (ttp80) REVERT: S 12 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8124 (ptmm) REVERT: S 120 GLN cc_start: 0.8330 (pp30) cc_final: 0.7622 (pp30) REVERT: B 75 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.7458 (mmt) REVERT: B 247 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8465 (tm-30) REVERT: O 90 ASP cc_start: 0.7557 (m-30) cc_final: 0.7309 (m-30) REVERT: C 183 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8104 (m) REVERT: R 24 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7275 (ttm110) REVERT: L 56 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8554 (mtm110) outliers start: 46 outliers final: 17 residues processed: 333 average time/residue: 1.5746 time to fit residues: 575.1898 Evaluate side-chains 327 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 305 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 295 ASN ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN R 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17178 Z= 0.352 Angle : 0.719 10.379 23311 Z= 0.335 Chirality : 0.049 0.778 2927 Planarity : 0.004 0.044 2774 Dihedral : 10.904 101.024 4437 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.19 % Allowed : 19.34 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1916 helix: 1.36 (0.29), residues: 353 sheet: 0.62 (0.23), residues: 524 loop : -0.23 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 109 HIS 0.004 0.001 HIS a 305 PHE 0.016 0.001 PHE a 399 TYR 0.016 0.001 TYR T 91 ARG 0.012 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 308 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7268 (ttp80) REVERT: S 12 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8189 (ptmm) REVERT: S 120 GLN cc_start: 0.8351 (pp30) cc_final: 0.7626 (pp30) REVERT: O 38 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8364 (ttm170) REVERT: R 24 ARG cc_start: 0.7662 (ttm110) cc_final: 0.7301 (ttm110) outliers start: 54 outliers final: 25 residues processed: 338 average time/residue: 1.5704 time to fit residues: 581.1204 Evaluate side-chains 330 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 302 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain a residue 396 GLU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 91 optimal weight: 0.0000 chunk 17 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN T 100 GLN B 185 ASN B 189 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17178 Z= 0.191 Angle : 0.664 9.771 23311 Z= 0.309 Chirality : 0.046 0.701 2927 Planarity : 0.004 0.051 2774 Dihedral : 10.291 100.643 4437 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.66 % Allowed : 20.58 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1916 helix: 1.53 (0.29), residues: 353 sheet: 0.75 (0.23), residues: 518 loop : -0.19 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 210 HIS 0.002 0.001 HIS A 141 PHE 0.013 0.001 PHE R 83 TYR 0.013 0.001 TYR Q 32 ARG 0.017 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 311 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7254 (ttp80) REVERT: T 30 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7939 (pp) REVERT: S 12 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8150 (ptmm) REVERT: c 414 MET cc_start: 0.8318 (tmm) cc_final: 0.7815 (ttp) REVERT: R 24 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7248 (ttm110) outliers start: 45 outliers final: 23 residues processed: 339 average time/residue: 1.5184 time to fit residues: 564.9760 Evaluate side-chains 331 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 305 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 170 optimal weight: 0.0060 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN B 185 ASN B 189 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN R 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17178 Z= 0.246 Angle : 0.677 9.748 23311 Z= 0.317 Chirality : 0.046 0.717 2927 Planarity : 0.004 0.054 2774 Dihedral : 9.886 100.020 4437 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.42 % Allowed : 21.23 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.20), residues: 1916 helix: 1.53 (0.29), residues: 353 sheet: 0.74 (0.23), residues: 518 loop : -0.21 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 210 HIS 0.003 0.001 HIS a 305 PHE 0.013 0.001 PHE a 399 TYR 0.013 0.001 TYR T 91 ARG 0.014 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 308 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7267 (ttp80) REVERT: S 12 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8175 (ptmm) REVERT: O 38 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8423 (ttm170) REVERT: R 24 ARG cc_start: 0.7642 (ttm110) cc_final: 0.7288 (ttm110) outliers start: 41 outliers final: 25 residues processed: 334 average time/residue: 1.6019 time to fit residues: 587.1384 Evaluate side-chains 337 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 309 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain R residue 100 GLN Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 100 GLN B 185 ASN B 189 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN R 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17178 Z= 0.212 Angle : 0.672 9.788 23311 Z= 0.314 Chirality : 0.046 0.701 2927 Planarity : 0.004 0.060 2774 Dihedral : 9.732 99.733 4437 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 1.95 % Allowed : 21.41 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1916 helix: 1.58 (0.29), residues: 353 sheet: 0.73 (0.23), residues: 518 loop : -0.20 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 210 HIS 0.002 0.001 HIS a 305 PHE 0.012 0.001 PHE b 399 TYR 0.026 0.001 TYR P 49 ARG 0.017 0.001 ARG a 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3832 Ramachandran restraints generated. 1916 Oldfield, 0 Emsley, 1916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 308 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 24 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7247 (ttp80) REVERT: S 12 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8167 (ptmm) REVERT: c 414 MET cc_start: 0.8324 (tmm) cc_final: 0.7817 (ttp) REVERT: R 24 ARG cc_start: 0.7628 (ttm110) cc_final: 0.7276 (ttm110) outliers start: 33 outliers final: 24 residues processed: 329 average time/residue: 1.5842 time to fit residues: 572.5109 Evaluate side-chains 332 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 306 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 4 LEU Chi-restraints excluded: chain R residue 21 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN B 189 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.064867 restraints weight = 33014.676| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.42 r_work: 0.2765 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17178 Z= 0.287 Angle : 0.697 9.641 23311 Z= 0.327 Chirality : 0.047 0.735 2927 Planarity : 0.004 0.054 2774 Dihedral : 9.598 99.634 4437 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.95 % Allowed : 21.88 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1916 helix: 1.49 (0.29), residues: 353 sheet: 0.71 (0.23), residues: 518 loop : -0.23 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 210 HIS 0.003 0.001 HIS a 305 PHE 0.014 0.001 PHE a 399 TYR 0.027 0.001 TYR P 49 ARG 0.017 0.001 ARG a 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8377.92 seconds wall clock time: 151 minutes 39.05 seconds (9099.05 seconds total)