Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 07:20:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uot_26653/04_2023/7uot_26653.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uot_26653/04_2023/7uot_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_2023/7uot_26653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uot_26653/04_2023/7uot_26653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uot_26653/04_2023/7uot_26653.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uot_26653/04_2023/7uot_26653.pdb" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 6 Time building chain proxies: 8.51, per 1000 atoms: 0.51 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: 8.21 Conformation dependent library (CDL) restraints added in 2.4 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: 1.28 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: 6.25 Time building geometry restraints manager: 8.80 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 - 17.95: 8376 17.95 - 35.91: 741 35.91 - 53.86: 135 53.86 - 71.82: 31 71.82 - 89.77: 13 Dihedral angle restraints: 9296 sinusoidal: 3642 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 9293 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: 9.620 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: 0.010 Extract box with map and model: 30.460 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 46.150 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.510 ------------------------------------------------------------------------------- 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 : 14.112 89.770 5608 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 % 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 *********************** 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 : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 341 average time/residue: 1.5756 time to fit residues: 587.1403 Evaluate side-chains 308 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 306 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.3092 time to fit residues: 3.5220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 189 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 295 ASN P 31 ASN 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: 0.8494 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 17178 Z= 0.374 Angle : 0.695 10.428 23311 Z= 0.335 Chirality : 0.048 0.701 2927 Planarity : 0.004 0.043 2774 Dihedral : 4.648 22.164 2125 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 1.77 % 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: 0.39 (0.20), residues: 1916 helix: 1.17 (0.29), residues: 350 sheet: 0.81 (0.23), residues: 528 loop : -0.31 (0.20), residues: 1038 *********************** 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 : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 9 residues processed: 321 average time/residue: 1.5500 time to fit residues: 544.2949 Evaluate side-chains 318 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 309 time to evaluate : 1.724 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 2 residues processed: 7 average time/residue: 0.6215 time to fit residues: 7.6907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 144 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 172 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN a 348 GLN B 185 ASN B 189 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 295 ASN P 31 ASN O 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 17178 Z= 0.179 Angle : 0.598 11.595 23311 Z= 0.286 Chirality : 0.043 0.574 2927 Planarity : 0.003 0.041 2774 Dihedral : 4.382 21.521 2125 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 1.83 % 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: 0.51 (0.20), residues: 1916 helix: 1.41 (0.29), residues: 353 sheet: 0.73 (0.24), residues: 524 loop : -0.19 (0.20), residues: 1039 *********************** 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 347 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 316 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 325 average time/residue: 1.4934 time to fit residues: 533.7672 Evaluate side-chains 316 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 304 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 8 average time/residue: 0.7819 time to fit residues: 9.8713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 90 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 0.0060 chunk 116 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- 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: 0.8507 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 17178 Z= 0.382 Angle : 0.690 13.403 23311 Z= 0.330 Chirality : 0.047 0.650 2927 Planarity : 0.004 0.044 2774 Dihedral : 4.606 23.359 2125 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 2.60 % 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: 1.34 (0.29), residues: 350 sheet: 0.61 (0.23), residues: 530 loop : -0.23 (0.20), residues: 1036 *********************** 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: 44 poor density : 310 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 16 residues processed: 328 average time/residue: 1.5441 time to fit residues: 555.5323 Evaluate side-chains 320 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 304 time to evaluate : 1.907 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 9 average time/residue: 0.5919 time to fit residues: 9.0748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8480 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 17178 Z= 0.250 Angle : 0.634 10.179 23311 Z= 0.303 Chirality : 0.044 0.600 2927 Planarity : 0.004 0.042 2774 Dihedral : 4.495 22.558 2125 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 2.66 % 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: 0.44 (0.20), residues: 1916 helix: 1.39 (0.29), residues: 353 sheet: 0.66 (0.23), residues: 524 loop : -0.23 (0.20), residues: 1039 *********************** 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 356 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 311 time to evaluate : 1.874 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 18 residues processed: 332 average time/residue: 1.5265 time to fit residues: 556.0729 Evaluate side-chains 319 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 301 time to evaluate : 1.846 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 7 average time/residue: 0.2336 time to fit residues: 4.9053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 17178 Z= 0.220 Angle : 0.619 10.878 23311 Z= 0.297 Chirality : 0.043 0.557 2927 Planarity : 0.004 0.045 2774 Dihedral : 4.403 22.657 2125 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 2.96 % 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: 0.48 (0.20), residues: 1916 helix: 1.44 (0.29), residues: 353 sheet: 0.67 (0.23), residues: 524 loop : -0.21 (0.20), residues: 1039 *********************** 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 357 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 307 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 22 residues processed: 334 average time/residue: 1.5231 time to fit residues: 562.1133 Evaluate side-chains 324 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 302 time to evaluate : 1.915 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 15 residues processed: 8 average time/residue: 0.7817 time to fit residues: 9.9944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 112 optimal weight: 0.0570 chunk 84 optimal weight: 1.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 17178 Z= 0.349 Angle : 0.677 10.450 23311 Z= 0.325 Chirality : 0.045 0.599 2927 Planarity : 0.004 0.048 2774 Dihedral : 4.551 23.380 2125 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 2.90 % 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: 1.35 (0.29), residues: 353 sheet: 0.65 (0.23), residues: 524 loop : -0.26 (0.20), residues: 1039 *********************** 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 353 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 304 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 25 residues processed: 335 average time/residue: 1.4783 time to fit residues: 544.1757 Evaluate side-chains 325 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 300 time to evaluate : 1.755 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 18 residues processed: 8 average time/residue: 0.5155 time to fit residues: 7.7022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 335 GLN T 100 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 17178 Z= 0.197 Angle : 0.625 9.606 23311 Z= 0.300 Chirality : 0.043 0.529 2927 Planarity : 0.004 0.052 2774 Dihedral : 4.401 22.512 2125 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 2.66 % 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: 0.54 (0.20), residues: 1916 helix: 1.52 (0.29), residues: 353 sheet: 0.78 (0.24), residues: 518 loop : -0.22 (0.20), residues: 1045 *********************** 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 355 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 310 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 26 residues processed: 338 average time/residue: 1.4832 time to fit residues: 551.7787 Evaluate side-chains 331 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 305 time to evaluate : 1.903 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 9 average time/residue: 0.5093 time to fit residues: 8.2516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 0.3980 chunk 52 optimal weight: 9.9990 chunk 155 optimal weight: 0.5980 chunk 162 optimal weight: 6.9990 chunk 170 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 17178 Z= 0.182 Angle : 0.616 9.714 23311 Z= 0.296 Chirality : 0.042 0.482 2927 Planarity : 0.004 0.054 2774 Dihedral : 4.294 22.267 2125 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 1.95 % 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: 0.60 (0.20), residues: 1916 helix: 1.61 (0.29), residues: 353 sheet: 0.81 (0.24), residues: 518 loop : -0.20 (0.20), residues: 1045 *********************** 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 342 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 309 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 22 residues processed: 334 average time/residue: 1.5377 time to fit residues: 566.0339 Evaluate side-chains 323 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 301 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 4 average time/residue: 0.6863 time to fit residues: 5.8549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.4980 chunk 181 optimal weight: 0.0000 chunk 110 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 c 348 GLN R 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 17178 Z= 0.174 Angle : 0.610 9.817 23311 Z= 0.293 Chirality : 0.042 0.455 2927 Planarity : 0.004 0.053 2774 Dihedral : 4.221 21.860 2125 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 1.42 % 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: 0.65 (0.20), residues: 1916 helix: 1.65 (0.29), residues: 353 sheet: 0.86 (0.24), residues: 518 loop : -0.18 (0.20), residues: 1045 ********************** 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 333 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 309 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 330 average time/residue: 1.5351 time to fit residues: 557.2974 Evaluate side-chains 322 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 303 time to evaluate : 1.903 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 2 average time/residue: 0.9113 time to fit residues: 4.4996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 247 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.093144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.066221 restraints weight = 32806.213| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.37 r_work: 0.2795 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 17178 Z= 0.227 Angle : 0.631 10.024 23311 Z= 0.303 Chirality : 0.042 0.480 2927 Planarity : 0.004 0.055 2774 Dihedral : 4.285 22.553 2125 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 2.07 % 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: 0.60 (0.20), residues: 1916 helix: 1.62 (0.29), residues: 353 sheet: 0.83 (0.23), residues: 518 loop : -0.21 (0.20), residues: 1045 =============================================================================== Job complete usr+sys time: 8034.74 seconds wall clock time: 143 minutes 43.25 seconds (8623.25 seconds total)